Starting phenix.real_space_refine on Sat Dec 9 11:51:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uif_26544/12_2023/7uif_26544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uif_26544/12_2023/7uif_26544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uif_26544/12_2023/7uif_26544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uif_26544/12_2023/7uif_26544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uif_26544/12_2023/7uif_26544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uif_26544/12_2023/7uif_26544.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 313 5.16 5 C 39981 2.51 5 N 10825 2.21 5 O 12018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A ASP 739": "OD1" <-> "OD2" Residue "A PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1206": "OD1" <-> "OD2" Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 550": "OD1" <-> "OD2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "C ASP 19": "OD1" <-> "OD2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "G ASP 65": "OD1" <-> "OD2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "M TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "S TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 9": "OE1" <-> "OE2" Residue "a GLU 16": "OE1" <-> "OE2" Residue "a TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 29": "OE1" <-> "OE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a GLU 45": "OE1" <-> "OE2" Residue "a GLU 46": "OE1" <-> "OE2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "a GLU 99": "OE1" <-> "OE2" Residue "a TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 170": "OE1" <-> "OE2" Residue "a TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 209": "OE1" <-> "OE2" Residue "a GLU 218": "OE1" <-> "OE2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 230": "OE1" <-> "OE2" Residue "a TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 236": "OE1" <-> "OE2" Residue "a GLU 243": "OE1" <-> "OE2" Residue "a GLU 246": "OE1" <-> "OE2" Residue "a GLU 257": "OE1" <-> "OE2" Residue "a PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 275": "OE1" <-> "OE2" Residue "a PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 281": "OE1" <-> "OE2" Residue "a PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 340": "OE1" <-> "OE2" Residue "a GLU 534": "OE1" <-> "OE2" Residue "a GLU 544": "OE1" <-> "OE2" Residue "a GLU 559": "OE1" <-> "OE2" Residue "a PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 35": "OD1" <-> "OD2" Residue "d GLU 82": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 114": "OE1" <-> "OE2" Residue "f TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 180": "OE1" <-> "OE2" Residue "h GLU 124": "OE1" <-> "OE2" Residue "i PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 88": "OE1" <-> "OE2" Residue "n TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 8": "OE1" <-> "OE2" Residue "w TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 105": "OE1" <-> "OE2" Residue "z TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 63137 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 11425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1453, 11425 Classifications: {'peptide': 1453} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1386} Chain: "B" Number of atoms: 9336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9336 Classifications: {'peptide': 1172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1120} Chain breaks: 3 Chain: "C" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2133 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1760 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "F" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1126 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain breaks: 1 Chain: "I" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 578 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "K" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 929 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 263 Classifications: {'peptide': 35} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 31} Chain: "P" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 861 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "Q" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1033 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain breaks: 1 Chain: "S" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "a" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3008 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 356} Chain breaks: 3 Chain: "d" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1388 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 2 Chain: "f" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1407 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 159} Chain breaks: 2 Chain: "g" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1409 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain breaks: 4 Chain: "h" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 1 Chain: "i" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 709 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 Chain: "j" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "k" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "n" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5139 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 18, 'TRANS': 606} Chain breaks: 6 Chain: "q" Number of atoms: 4182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4182 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 497} Chain breaks: 4 Chain: "r" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1995 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain breaks: 1 Chain: "s" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "t" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1609 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "u" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "v" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 869 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "w" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 871 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Chain: "z" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 6, 'TRANS': 18} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N PRO z 8 " occ=0.70 ... (5 atoms not shown) pdb=" CD PRO z 8 " occ=0.70 residue: pdb=" N SER z 9 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER z 9 " occ=0.70 Time building chain proxies: 23.45, per 1000 atoms: 0.37 Number of scatterers: 63137 At special positions: 0 Unit cell: (226.32, 251.16, 258.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 313 16.00 O 12018 8.00 N 10825 7.00 C 39981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 88 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.64 Conformation dependent library (CDL) restraints added in 8.2 seconds 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14986 Finding SS restraints... Secondary structure from input PDB file: 279 helices and 70 sheets defined 46.8% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 260 through 281 removed outlier: 3.513A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 305 removed outlier: 3.856A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.567A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.765A pdb=" N LEU A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.695A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.562A pdb=" N VAL A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.764A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 672 through 698 Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.869A pdb=" N LEU A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.831A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.629A pdb=" N ASP A 871 " --> pdb=" O TYR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 903 through 907 removed outlier: 3.989A pdb=" N THR A 907 " --> pdb=" O THR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.894A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.283A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1055 removed outlier: 3.532A pdb=" N ARG A1055 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 removed outlier: 3.609A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix removed outlier: 3.777A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1081 No H-bonds generated for 'chain 'A' and resid 1080 through 1081' Processing helix chain 'A' and resid 1082 through 1093 removed outlier: 3.538A pdb=" N HIS A1085 " --> pdb=" O ASN A1082 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A1086 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA A1090 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A1091 " --> pdb=" O GLY A1088 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A1093 " --> pdb=" O ALA A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.854A pdb=" N ALA A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1175 removed outlier: 3.619A pdb=" N GLU A1168 " --> pdb=" O PRO A1164 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1186 through 1188 No H-bonds generated for 'chain 'A' and resid 1186 through 1188' Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.685A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1222 removed outlier: 3.519A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS A1217 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1255 through 1270 removed outlier: 3.935A pdb=" N LYS A1262 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.585A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.957A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1390 Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.568A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.669A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.604A pdb=" N ILE B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.899A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 184 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.900A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.363A pdb=" N ALA B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 360 removed outlier: 3.705A pdb=" N LEU B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.561A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.666A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.767A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.817A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.839A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.099A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.706A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.504A pdb=" N HIS B 761 " --> pdb=" O PHE B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 808 through 813 removed outlier: 3.713A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 889 through 893 removed outlier: 4.233A pdb=" N LYS B 892 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.761A pdb=" N ALA B1016 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.811A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.502A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1209 removed outlier: 3.777A pdb=" N LYS B1201 " --> pdb=" O PRO B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1223 removed outlier: 3.861A pdb=" N ASP B1223 " --> pdb=" O ARG B1220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1223' Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.689A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 68 removed outlier: 4.002A pdb=" N ILE C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.541A pdb=" N LEU C 80 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.627A pdb=" N TRP C 170 " --> pdb=" O HIS C 167 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.766A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.900A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 271 Processing helix chain 'D' and resid 51 through 78 Processing helix chain 'D' and resid 110 through 115 removed outlier: 4.131A pdb=" N MET D 114 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 115' Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.613A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.894A pdb=" N GLU E 6 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.536A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 123 through 127 removed outlier: 4.368A pdb=" N ILE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.595A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.822A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.641A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.646A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.590A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.734A pdb=" N SER I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.664A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU J 24 " --> pdb=" O SER J 20 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.764A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.540A pdb=" N ARG J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.670A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.610A pdb=" N GLU K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.579A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 116 Processing helix chain 'P' and resid 107 through 113 removed outlier: 4.531A pdb=" N ASN P 113 " --> pdb=" O GLU P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 133 Processing helix chain 'Q' and resid 74 through 82 Processing helix chain 'Q' and resid 83 through 88 removed outlier: 3.714A pdb=" N ASN Q 86 " --> pdb=" O ASP Q 83 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS Q 88 " --> pdb=" O ASN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 247 removed outlier: 3.654A pdb=" N LYS Q 235 " --> pdb=" O PRO Q 231 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Q 246 " --> pdb=" O ASN Q 242 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN Q 247 " --> pdb=" O ILE Q 243 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 138 Processing helix chain 'S' and resid 146 through 163 removed outlier: 4.591A pdb=" N GLU S 163 " --> pdb=" O VAL S 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.652A pdb=" N ILE S 171 " --> pdb=" O PRO S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 208 Processing helix chain 'S' and resid 212 through 221 removed outlier: 3.709A pdb=" N HIS S 216 " --> pdb=" O PRO S 212 " (cutoff:3.500A) Processing helix chain 'S' and resid 224 through 231 Processing helix chain 'S' and resid 238 through 256 Processing helix chain 'a' and resid 7 through 22 Processing helix chain 'a' and resid 27 through 38 Processing helix chain 'a' and resid 102 through 110 Processing helix chain 'a' and resid 114 through 131 Processing helix chain 'a' and resid 163 through 182 removed outlier: 3.802A pdb=" N SER a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS a 173 " --> pdb=" O THR a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 281 No H-bonds generated for 'chain 'a' and resid 279 through 281' Processing helix chain 'a' and resid 297 through 305 Processing helix chain 'a' and resid 331 through 335 Processing helix chain 'a' and resid 336 through 351 removed outlier: 4.256A pdb=" N GLU a 340 " --> pdb=" O ASP a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 361 Processing helix chain 'a' and resid 550 through 566 Processing helix chain 'd' and resid 32 through 40 removed outlier: 3.845A pdb=" N VAL d 40 " --> pdb=" O LYS d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 62 removed outlier: 4.030A pdb=" N GLU d 44 " --> pdb=" O VAL d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 89 removed outlier: 3.560A pdb=" N ALA d 70 " --> pdb=" O ASN d 66 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA d 88 " --> pdb=" O VAL d 84 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU d 89 " --> pdb=" O LYS d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 128 Processing helix chain 'd' and resid 132 through 148 removed outlier: 3.520A pdb=" N ILE d 148 " --> pdb=" O GLN d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 165 removed outlier: 3.680A pdb=" N LEU d 153 " --> pdb=" O ASN d 149 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS d 162 " --> pdb=" O THR d 158 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE d 163 " --> pdb=" O LYS d 159 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS d 165 " --> pdb=" O SER d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 191 Processing helix chain 'd' and resid 191 through 199 removed outlier: 4.359A pdb=" N MET d 195 " --> pdb=" O GLY d 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 20 Processing helix chain 'f' and resid 26 through 33 removed outlier: 4.389A pdb=" N GLU f 33 " --> pdb=" O ASP f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 56 removed outlier: 3.719A pdb=" N VAL f 45 " --> pdb=" O SER f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 89 through 97 removed outlier: 3.877A pdb=" N TYR f 97 " --> pdb=" O ILE f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 108 removed outlier: 3.660A pdb=" N MET f 101 " --> pdb=" O TYR f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 192 Processing helix chain 'g' and resid 18 through 23 removed outlier: 3.728A pdb=" N PHE g 23 " --> pdb=" O VAL g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 43 Proline residue: g 32 - end of helix Processing helix chain 'g' and resid 112 through 140 Processing helix chain 'g' and resid 141 through 143 No H-bonds generated for 'chain 'g' and resid 141 through 143' Processing helix chain 'g' and resid 144 through 166 removed outlier: 3.640A pdb=" N GLU g 149 " --> pdb=" O GLU g 145 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN g 150 " --> pdb=" O ARG g 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU g 164 " --> pdb=" O HIS g 160 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR g 165 " --> pdb=" O LEU g 161 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 213 Processing helix chain 'h' and resid 31 through 55 Processing helix chain 'h' and resid 61 through 86 Processing helix chain 'h' and resid 86 through 93 Processing helix chain 'h' and resid 102 through 115 removed outlier: 6.453A pdb=" N SER h 108 " --> pdb=" O THR h 104 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU h 109 " --> pdb=" O SER h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 119 through 134 Processing helix chain 'h' and resid 144 through 170 removed outlier: 3.818A pdb=" N HIS h 170 " --> pdb=" O GLU h 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 79 Processing helix chain 'i' and resid 83 through 108 removed outlier: 3.830A pdb=" N ASN i 108 " --> pdb=" O LEU i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 115 removed outlier: 3.629A pdb=" N LYS i 112 " --> pdb=" O ASN i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 148 removed outlier: 3.500A pdb=" N GLN i 148 " --> pdb=" O TYR i 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 38 Processing helix chain 'j' and resid 42 through 68 Processing helix chain 'j' and resid 80 through 87 Processing helix chain 'j' and resid 94 through 133 Processing helix chain 'j' and resid 136 through 148 Processing helix chain 'k' and resid 3 through 40 removed outlier: 3.523A pdb=" N GLN k 7 " --> pdb=" O PRO k 3 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY k 35 " --> pdb=" O THR k 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU k 36 " --> pdb=" O PHE k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 77 removed outlier: 3.531A pdb=" N PHE k 48 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU k 49 " --> pdb=" O LYS k 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN k 50 " --> pdb=" O PRO k 46 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER k 62 " --> pdb=" O ARG k 58 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR k 63 " --> pdb=" O LEU k 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU k 75 " --> pdb=" O GLN k 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL k 77 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 110 removed outlier: 3.997A pdb=" N ASP k 94 " --> pdb=" O ALA k 90 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR k 95 " --> pdb=" O LEU k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 114 removed outlier: 3.717A pdb=" N SER k 114 " --> pdb=" O PRO k 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 111 through 114' Processing helix chain 'n' and resid 91 through 117 Processing helix chain 'n' and resid 122 through 154 removed outlier: 3.613A pdb=" N LYS n 126 " --> pdb=" O PRO n 122 " (cutoff:3.500A) Processing helix chain 'n' and resid 161 through 191 Processing helix chain 'n' and resid 241 through 260 Processing helix chain 'n' and resid 263 through 267 Processing helix chain 'n' and resid 344 through 359 Processing helix chain 'n' and resid 365 through 393 removed outlier: 3.700A pdb=" N ASN n 391 " --> pdb=" O LEU n 387 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY n 392 " --> pdb=" O LYS n 388 " (cutoff:3.500A) Processing helix chain 'n' and resid 444 through 450 Processing helix chain 'n' and resid 459 through 486 removed outlier: 6.468A pdb=" N GLU n 465 " --> pdb=" O VAL n 461 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY n 466 " --> pdb=" O SER n 462 " (cutoff:3.500A) Processing helix chain 'n' and resid 530 through 542 Processing helix chain 'n' and resid 545 through 571 Processing helix chain 'n' and resid 684 through 711 removed outlier: 4.009A pdb=" N LEU n 696 " --> pdb=" O GLN n 692 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN n 697 " --> pdb=" O ARG n 693 " (cutoff:3.500A) Processing helix chain 'n' and resid 719 through 725 Processing helix chain 'n' and resid 729 through 734 Processing helix chain 'n' and resid 749 through 753 Processing helix chain 'n' and resid 756 through 760 removed outlier: 3.853A pdb=" N LEU n 759 " --> pdb=" O SER n 756 " (cutoff:3.500A) Processing helix chain 'n' and resid 788 through 792 Processing helix chain 'n' and resid 795 through 798 Processing helix chain 'n' and resid 818 through 820 No H-bonds generated for 'chain 'n' and resid 818 through 820' Processing helix chain 'n' and resid 821 through 832 Processing helix chain 'q' and resid 91 through 97 Processing helix chain 'q' and resid 98 through 111 Proline residue: q 104 - end of helix Processing helix chain 'q' and resid 120 through 133 Processing helix chain 'q' and resid 198 through 226 removed outlier: 3.735A pdb=" N GLU q 217 " --> pdb=" O LEU q 213 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER q 218 " --> pdb=" O ALA q 214 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU q 220 " --> pdb=" O ASN q 216 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA q 221 " --> pdb=" O GLU q 217 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU q 222 " --> pdb=" O SER q 218 " (cutoff:3.500A) Processing helix chain 'q' and resid 226 through 233 removed outlier: 3.823A pdb=" N SER q 230 " --> pdb=" O SER q 226 " (cutoff:3.500A) Processing helix chain 'q' and resid 233 through 239 removed outlier: 4.450A pdb=" N SER q 239 " --> pdb=" O SER q 235 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 249 removed outlier: 3.546A pdb=" N VAL q 249 " --> pdb=" O LEU q 245 " (cutoff:3.500A) Processing helix chain 'q' and resid 265 through 316 removed outlier: 4.437A pdb=" N TYR q 269 " --> pdb=" O THR q 265 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE q 270 " --> pdb=" O LYS q 266 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU q 271 " --> pdb=" O LYS q 267 " (cutoff:3.500A) Processing helix chain 'q' and resid 341 through 345 removed outlier: 3.817A pdb=" N GLY q 345 " --> pdb=" O GLU q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 380 through 386 Processing helix chain 'q' and resid 417 through 422 Processing helix chain 'q' and resid 424 through 450 Processing helix chain 'q' and resid 451 through 455 removed outlier: 4.946A pdb=" N SER q 454 " --> pdb=" O LEU q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 497 through 526 removed outlier: 3.640A pdb=" N SER q 526 " --> pdb=" O SER q 522 " (cutoff:3.500A) Processing helix chain 'q' and resid 541 through 566 removed outlier: 4.458A pdb=" N ILE q 545 " --> pdb=" O ILE q 541 " (cutoff:3.500A) Processing helix chain 'q' and resid 593 through 605 removed outlier: 3.567A pdb=" N THR q 597 " --> pdb=" O ASP q 593 " (cutoff:3.500A) Processing helix chain 'q' and resid 606 through 611 Processing helix chain 'q' and resid 666 through 686 Processing helix chain 'r' and resid 15 through 28 Processing helix chain 'r' and resid 71 through 75 Processing helix chain 'r' and resid 86 through 93 removed outlier: 3.606A pdb=" N ILE r 89 " --> pdb=" O ASN r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 109 Processing helix chain 'r' and resid 199 through 208 Processing helix chain 'r' and resid 225 through 227 No H-bonds generated for 'chain 'r' and resid 225 through 227' Processing helix chain 'r' and resid 264 through 282 removed outlier: 3.865A pdb=" N ILE r 268 " --> pdb=" O ASP r 264 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 47 Processing helix chain 's' and resid 64 through 68 Processing helix chain 's' and resid 134 through 148 Processing helix chain 't' and resid 15 through 24 Processing helix chain 't' and resid 83 through 87 removed outlier: 3.872A pdb=" N ILE t 87 " --> pdb=" O ALA t 84 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 95 removed outlier: 3.607A pdb=" N VAL t 92 " --> pdb=" O PRO t 88 " (cutoff:3.500A) Processing helix chain 't' and resid 103 through 111 removed outlier: 3.544A pdb=" N ILE t 107 " --> pdb=" O SER t 103 " (cutoff:3.500A) Processing helix chain 't' and resid 162 through 177 removed outlier: 3.647A pdb=" N ILE t 177 " --> pdb=" O HIS t 173 " (cutoff:3.500A) Processing helix chain 't' and resid 195 through 209 Processing helix chain 'u' and resid 3 through 30 Processing helix chain 'u' and resid 51 through 78 Processing helix chain 'u' and resid 86 through 138 removed outlier: 3.600A pdb=" N GLN u 90 " --> pdb=" O SER u 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 29 Processing helix chain 'v' and resid 46 through 87 removed outlier: 4.072A pdb=" N ALA v 51 " --> pdb=" O GLU v 47 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN v 87 " --> pdb=" O TRP v 83 " (cutoff:3.500A) Processing helix chain 'v' and resid 101 through 119 Processing helix chain 'w' and resid 21 through 33 Processing helix chain 'w' and resid 35 through 45 removed outlier: 3.627A pdb=" N GLN w 45 " --> pdb=" O TYR w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 45 through 51 removed outlier: 4.090A pdb=" N TRP w 49 " --> pdb=" O GLN w 45 " (cutoff:3.500A) Processing helix chain 'w' and resid 51 through 61 removed outlier: 4.166A pdb=" N LYS w 55 " --> pdb=" O SER w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 62 through 66 removed outlier: 4.137A pdb=" N ASN w 66 " --> pdb=" O TYR w 63 " (cutoff:3.500A) Processing helix chain 'w' and resid 68 through 73 removed outlier: 3.530A pdb=" N ILE w 73 " --> pdb=" O SER w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 89 removed outlier: 3.933A pdb=" N PHE w 80 " --> pdb=" O PRO w 76 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS w 83 " --> pdb=" O LEU w 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET w 89 " --> pdb=" O LEU w 85 " (cutoff:3.500A) Processing helix chain 'w' and resid 105 through 126 Proline residue: w 115 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 6.876A pdb=" N TYR B1217 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 17 " --> pdb=" O ARG B1215 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG B1215 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 7.024A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.572A pdb=" N GLN A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.516A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 367 removed outlier: 6.219A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B1104 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.858A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.686A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 567 removed outlier: 5.840A pdb=" N ILE A 565 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR H 98 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU H 27 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.726A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 removed outlier: 3.527A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.872A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 3.545A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1147 through 1154 removed outlier: 8.176A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.334A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.487A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.697A pdb=" N VAL B 237 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 280 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 3.614A pdb=" N GLU B 564 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 589 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 643 Processing sheet with id=AD1, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 853 through 862 current: chain 'B' and resid 947 through 956 removed outlier: 6.533A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 962 through 972 current: chain 'L' and resid 37 through 38 Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.568A pdb=" N MET B 839 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR B 994 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N MET B 841 " --> pdb=" O TYR B 994 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.520A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.352A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 43 through 54 removed outlier: 5.734A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.551A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.695A pdb=" N LEU D 50 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.684A pdb=" N TYR E 112 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.546A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 169 through 170 removed outlier: 4.200A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 144 " --> pdb=" O GLY G 169 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.652A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.551A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 103 through 105 Processing sheet with id=AF6, first strand: chain 'P' and resid 117 through 121 removed outlier: 6.069A pdb=" N LEU P 118 " --> pdb=" O TYR P 393 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE P 395 " --> pdb=" O LEU P 118 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS P 120 " --> pdb=" O PHE P 395 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA P 397 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 67 through 72 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 67 through 72 current: chain 'Q' and resid 104 through 108 removed outlier: 4.013A pdb=" N ILE Q 104 " --> pdb=" O LEU Q 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 119 through 126 current: chain 'Q' and resid 211 through 226 Processing sheet with id=AF8, first strand: chain 'S' and resid 279 through 284 Processing sheet with id=AF9, first strand: chain 'a' and resid 41 through 46 removed outlier: 6.790A pdb=" N VAL a 62 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU a 79 " --> pdb=" O VAL a 62 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP a 64 " --> pdb=" O VAL a 77 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL a 77 " --> pdb=" O ASP a 64 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASP a 66 " --> pdb=" O GLN a 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 187 through 190 removed outlier: 6.381A pdb=" N ILE a 198 " --> pdb=" O LYS a 214 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS a 214 " --> pdb=" O ILE a 198 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE a 200 " --> pdb=" O LEU a 212 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 252 through 258 current: chain 'a' and resid 322 through 329 Processing sheet with id=AG2, first strand: chain 'a' and resid 227 through 229 Processing sheet with id=AG3, first strand: chain 'a' and resid 232 through 234 removed outlier: 3.653A pdb=" N SER a 239 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 312 through 316 Processing sheet with id=AG5, first strand: chain 'f' and resid 113 through 121 removed outlier: 3.888A pdb=" N GLN f 131 " --> pdb=" O GLU f 114 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL f 127 " --> pdb=" O SER f 118 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL f 120 " --> pdb=" O PHE f 125 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE f 125 " --> pdb=" O VAL f 120 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP f 126 " --> pdb=" O TYR f 154 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR f 154 " --> pdb=" O TRP f 126 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE f 128 " --> pdb=" O ASP f 152 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP f 152 " --> pdb=" O ILE f 128 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LYS f 130 " --> pdb=" O LEU f 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 193 through 195 Processing sheet with id=AG7, first strand: chain 'g' and resid 76 through 78 Processing sheet with id=AG8, first strand: chain 'n' and resid 269 through 272 removed outlier: 6.067A pdb=" N SER n 289 " --> pdb=" O PHE n 299 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE n 299 " --> pdb=" O SER n 289 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'n' and resid 400 through 405 removed outlier: 3.786A pdb=" N GLY n 425 " --> pdb=" O TYR n 415 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS n 426 " --> pdb=" O ASP n 443 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'n' and resid 490 through 491 Processing sheet with id=AH2, first strand: chain 'n' and resid 575 through 577 removed outlier: 4.871A pdb=" N PHE n 626 " --> pdb=" O SER n 577 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE n 655 " --> pdb=" O LEU n 670 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU n 670 " --> pdb=" O ILE n 655 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS n 657 " --> pdb=" O LYS n 668 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'n' and resid 715 through 717 removed outlier: 6.840A pdb=" N SER n 766 " --> pdb=" O LYS n 783 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS n 783 " --> pdb=" O SER n 766 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'q' and resid 321 through 326 removed outlier: 4.505A pdb=" N VAL q 321 " --> pdb=" O LYS q 338 " (cutoff:3.500A) removed outlier: 14.007A pdb=" N LYS q 333 " --> pdb=" O ASN q 359 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N ASN q 359 " --> pdb=" O LYS q 333 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU q 335 " --> pdb=" O ILE q 357 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 403 through 408 removed outlier: 6.011A pdb=" N LEU q 405 " --> pdb=" O THR q 395 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR q 395 " --> pdb=" O LEU q 405 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS q 464 " --> pdb=" O GLU q 460 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'q' and resid 574 through 578 Processing sheet with id=AH7, first strand: chain 'r' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 2 through 12 current: chain 'r' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 181 through 195 current: chain 'r' and resid 229 through 239 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 242 through 245 current: chain 't' and resid 56 through 62 WARNING: can't find start of bonding for strands! previous: chain 't' and resid 76 through 81 current: chain 't' and resid 135 through 143 removed outlier: 7.049A pdb=" N THR t 136 " --> pdb=" O LEU t 155 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU t 155 " --> pdb=" O THR t 136 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG t 138 " --> pdb=" O ILE t 153 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE t 153 " --> pdb=" O ARG t 138 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL t 140 " --> pdb=" O LEU t 151 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU t 151 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU t 142 " --> pdb=" O LYS t 149 " (cutoff:3.500A) 3065 hydrogen bonds defined for protein. 8727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.62 Time building geometry restraints manager: 19.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17264 1.33 - 1.46: 16897 1.46 - 1.59: 29578 1.59 - 1.72: 0 1.72 - 1.85: 510 Bond restraints: 64249 Sorted by residual: bond pdb=" CZ ARG a 189 " pdb=" NH2 ARG a 189 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.12e+00 bond pdb=" CZ ARG a 349 " pdb=" NH2 ARG a 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.12e+00 bond pdb=" CZ ARG a 33 " pdb=" NH2 ARG a 33 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.62e+00 bond pdb=" ND1 HIS a 536 " pdb=" CE1 HIS a 536 " ideal model delta sigma weight residual 1.321 1.346 -0.025 1.00e-02 1.00e+04 6.45e+00 bond pdb=" CD2 HIS a 173 " pdb=" NE2 HIS a 173 " ideal model delta sigma weight residual 1.374 1.402 -0.028 1.10e-02 8.26e+03 6.29e+00 ... (remaining 64244 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.27: 1159 105.27 - 112.58: 33497 112.58 - 119.89: 23081 119.89 - 127.20: 28444 127.20 - 134.51: 546 Bond angle restraints: 86727 Sorted by residual: angle pdb=" C GLN B 278 " pdb=" N ASP B 279 " pdb=" CA ASP B 279 " ideal model delta sigma weight residual 121.54 132.68 -11.14 1.91e+00 2.74e-01 3.40e+01 angle pdb=" CA PRO g 16 " pdb=" N PRO g 16 " pdb=" CD PRO g 16 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.14e+01 angle pdb=" C PRO a 298 " pdb=" N ILE a 299 " pdb=" CA ILE a 299 " ideal model delta sigma weight residual 120.56 127.43 -6.87 1.26e+00 6.30e-01 2.97e+01 angle pdb=" OE1 GLN a 529 " pdb=" CD GLN a 529 " pdb=" NE2 GLN a 529 " ideal model delta sigma weight residual 122.60 117.17 5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" C LYS a 22 " pdb=" N PRO a 23 " pdb=" CA PRO a 23 " ideal model delta sigma weight residual 119.56 124.79 -5.23 1.02e+00 9.61e-01 2.63e+01 ... (remaining 86722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 35566 17.66 - 35.31: 3357 35.31 - 52.97: 486 52.97 - 70.63: 85 70.63 - 88.28: 46 Dihedral angle restraints: 39540 sinusoidal: 16509 harmonic: 23031 Sorted by residual: dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual -86.00 -140.77 54.77 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CA CYS C 92 " pdb=" C CYS C 92 " pdb=" N ASP C 93 " pdb=" CA ASP C 93 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA SER a 295 " pdb=" C SER a 295 " pdb=" N SER a 296 " pdb=" CA SER a 296 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 39537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 8438 0.065 - 0.130: 1247 0.130 - 0.196: 109 0.196 - 0.261: 9 0.261 - 0.326: 2 Chirality restraints: 9805 Sorted by residual: chirality pdb=" CG LEU B 289 " pdb=" CB LEU B 289 " pdb=" CD1 LEU B 289 " pdb=" CD2 LEU B 289 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB VAL A1015 " pdb=" CA VAL A1015 " pdb=" CG1 VAL A1015 " pdb=" CG2 VAL A1015 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CG LEU i 73 " pdb=" CB LEU i 73 " pdb=" CD1 LEU i 73 " pdb=" CD2 LEU i 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 9802 not shown) Planarity restraints: 11160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a 216 " 0.109 2.00e-02 2.50e+03 6.76e-02 9.13e+01 pdb=" CG TYR a 216 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR a 216 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR a 216 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR a 216 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR a 216 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR a 216 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR a 216 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 344 " -0.088 2.00e-02 2.50e+03 4.66e-02 5.42e+01 pdb=" CG TRP a 344 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP a 344 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP a 344 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP a 344 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP a 344 " 0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 344 " -0.080 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP a 344 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 67 " 0.055 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR a 67 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR a 67 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR a 67 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR a 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR a 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR a 67 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR a 67 " 0.085 2.00e-02 2.50e+03 ... (remaining 11157 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 6 1.66 - 2.47: 291 2.47 - 3.28: 67153 3.28 - 4.09: 150055 4.09 - 4.90: 272195 Warning: very small nonbonded interaction distances. Nonbonded interactions: 489700 Sorted by model distance: nonbonded pdb=" CD2 TYR a 21 " pdb=" NZ LYS d 71 " model vdw 0.850 3.420 nonbonded pdb=" CE2 TYR a 21 " pdb=" NZ LYS d 71 " model vdw 1.176 3.420 nonbonded pdb=" CG TYR a 21 " pdb=" NZ LYS d 71 " model vdw 1.304 3.340 nonbonded pdb=" CZ TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.462 3.660 nonbonded pdb=" CE1 TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.614 3.740 ... (remaining 489695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 11.470 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 121.660 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 64249 Z= 0.272 Angle : 0.688 12.456 86727 Z= 0.393 Chirality : 0.046 0.326 9805 Planarity : 0.005 0.147 11160 Dihedral : 13.630 88.285 24545 Min Nonbonded Distance : 0.850 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 0.06 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.10), residues: 7715 helix: 1.40 (0.09), residues: 3216 sheet: 0.38 (0.15), residues: 1253 loop : -0.51 (0.11), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.004 TRP a 344 HIS 0.014 0.001 HIS a 536 PHE 0.055 0.002 PHE a 356 TYR 0.116 0.002 TYR a 216 ARG 0.011 0.001 ARG h 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1851 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1847 time to evaluate : 5.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 1851 average time/residue: 0.6630 time to fit residues: 1986.2660 Evaluate side-chains 1108 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1106 time to evaluate : 5.362 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4288 time to fit residues: 9.3433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 651 optimal weight: 10.0000 chunk 585 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 199 optimal weight: 0.2980 chunk 394 optimal weight: 20.0000 chunk 312 optimal weight: 3.9990 chunk 605 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 367 optimal weight: 1.9990 chunk 450 optimal weight: 7.9990 chunk 701 optimal weight: 0.0870 overall best weight: 2.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 71 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 GLN ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS A1367 HIS ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS B1187 ASN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 153 GLN H 83 GLN H 139 ASN K 96 ASN ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 ASN S 151 GLN ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN a 324 ASN a 529 GLN ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN h 70 ASN ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 165 ASN i 85 ASN ** j 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 402 HIS n 502 GLN n 635 ASN q 255 ASN q 303 GLN q 304 ASN q 314 GLN ** r 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 48 ASN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 60 ASN v 61 GLN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3993 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 64249 Z= 0.284 Angle : 0.728 12.345 86727 Z= 0.379 Chirality : 0.046 0.263 9805 Planarity : 0.006 0.152 11160 Dihedral : 4.749 33.110 8482 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 0.35 % Allowed : 5.22 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 7715 helix: 1.12 (0.09), residues: 3278 sheet: 0.27 (0.15), residues: 1191 loop : -0.36 (0.11), residues: 3246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 466 HIS 0.015 0.002 HIS B 761 PHE 0.038 0.002 PHE G 18 TYR 0.031 0.002 TYR A1349 ARG 0.029 0.001 ARG h 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1408 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1383 time to evaluate : 5.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 1405 average time/residue: 0.6423 time to fit residues: 1489.4984 Evaluate side-chains 1054 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1045 time to evaluate : 5.421 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4797 time to fit residues: 15.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 389 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 583 optimal weight: 0.1980 chunk 477 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 702 optimal weight: 0.9980 chunk 758 optimal weight: 6.9990 chunk 625 optimal weight: 20.0000 chunk 696 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 563 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 439 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS A1070 GLN A1211 GLN ** B 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 153 GLN H 139 ASN I 23 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 220 HIS ** Q 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN S 191 ASN S 205 ASN ** S 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 ASN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN ** d 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 182 ASN ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 51 HIS ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 701 ASN ** r 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 294 GLN ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 ASN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 86 ASN w 113 GLN w 116 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4055 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 64249 Z= 0.221 Angle : 0.620 10.521 86727 Z= 0.323 Chirality : 0.043 0.252 9805 Planarity : 0.005 0.104 11160 Dihedral : 4.568 29.827 8482 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 0.23 % Allowed : 3.59 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 7715 helix: 1.28 (0.09), residues: 3306 sheet: 0.17 (0.15), residues: 1193 loop : -0.24 (0.11), residues: 3216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP q 279 HIS 0.014 0.001 HIS E 146 PHE 0.041 0.002 PHE n 386 TYR 0.036 0.002 TYR A1349 ARG 0.023 0.001 ARG i 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1341 time to evaluate : 5.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 1352 average time/residue: 0.6341 time to fit residues: 1417.3051 Evaluate side-chains 1035 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1030 time to evaluate : 5.391 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5027 time to fit residues: 12.1154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 693 optimal weight: 0.8980 chunk 528 optimal weight: 4.9990 chunk 364 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 335 optimal weight: 0.0370 chunk 471 optimal weight: 20.0000 chunk 704 optimal weight: 0.5980 chunk 746 optimal weight: 9.9990 chunk 368 optimal weight: 8.9990 chunk 668 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 215 GLN B 309 GLN ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 587 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 153 GLN H 139 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 220 HIS S 151 GLN ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 HIS ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 GLN ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 277 ASN r 294 GLN ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN v 68 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4064 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 64249 Z= 0.186 Angle : 0.596 10.996 86727 Z= 0.310 Chirality : 0.043 0.203 9805 Planarity : 0.005 0.124 11160 Dihedral : 4.472 26.920 8482 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.25 % Rotamer: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 7715 helix: 1.39 (0.09), residues: 3305 sheet: 0.16 (0.15), residues: 1187 loop : -0.21 (0.11), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP q 279 HIS 0.008 0.001 HIS n 116 PHE 0.043 0.002 PHE i 70 TYR 0.033 0.001 TYR r 102 ARG 0.013 0.001 ARG B1150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1309 time to evaluate : 5.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 1317 average time/residue: 0.6313 time to fit residues: 1375.9278 Evaluate side-chains 1049 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1044 time to evaluate : 5.394 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5187 time to fit residues: 12.3573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 621 optimal weight: 9.9990 chunk 423 optimal weight: 0.0270 chunk 10 optimal weight: 0.9990 chunk 555 optimal weight: 20.0000 chunk 307 optimal weight: 1.9990 chunk 636 optimal weight: 1.9990 chunk 515 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 381 optimal weight: 8.9990 chunk 669 optimal weight: 0.0770 chunk 188 optimal weight: 9.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A1009 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN G 153 GLN H 33 GLN ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 220 HIS ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 383 HIS ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 226 HIS ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 277 ASN r 294 GLN ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4052 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 64249 Z= 0.166 Angle : 0.581 9.917 86727 Z= 0.301 Chirality : 0.043 0.221 9805 Planarity : 0.004 0.146 11160 Dihedral : 4.362 26.934 8482 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Rotamer: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 7715 helix: 1.47 (0.09), residues: 3299 sheet: 0.24 (0.15), residues: 1171 loop : -0.14 (0.11), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP q 279 HIS 0.009 0.001 HIS n 116 PHE 0.035 0.001 PHE A1410 TYR 0.027 0.001 TYR f 100 ARG 0.016 0.001 ARG A1012 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1316 time to evaluate : 5.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 1321 average time/residue: 0.6363 time to fit residues: 1393.1424 Evaluate side-chains 1037 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1033 time to evaluate : 5.414 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5152 time to fit residues: 11.3614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 251 optimal weight: 4.9990 chunk 672 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 438 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 746 optimal weight: 5.9990 chunk 620 optimal weight: 0.8980 chunk 345 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 392 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 358 ASN A 390 GLN A 510 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 ASN A1124 HIS A1183 GLN A1211 GLN A1218 GLN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 309 GLN ** B 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 481 GLN B 494 HIS B 515 HIS B 733 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS B1205 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN H 133 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN J 23 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN Q 220 HIS ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 346 GLN ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 71 GLN k 93 GLN n 173 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 631 HIS ** n 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 269 ASN r 294 GLN t 48 ASN ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 86 ASN w 46 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4435 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 64249 Z= 0.337 Angle : 0.772 14.267 86727 Z= 0.403 Chirality : 0.047 0.285 9805 Planarity : 0.006 0.092 11160 Dihedral : 4.969 27.831 8482 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 25.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 0.07 % Allowed : 2.93 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.09), residues: 7715 helix: 0.71 (0.09), residues: 3331 sheet: -0.14 (0.15), residues: 1186 loop : -0.40 (0.11), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP q 279 HIS 0.011 0.002 HIS G 14 PHE 0.036 0.003 PHE i 70 TYR 0.031 0.002 TYR B 830 ARG 0.025 0.001 ARG B 942 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1288 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 1292 average time/residue: 0.6512 time to fit residues: 1394.8642 Evaluate side-chains 991 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 989 time to evaluate : 5.712 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5838 time to fit residues: 9.8053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 720 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 425 optimal weight: 10.0000 chunk 545 optimal weight: 7.9990 chunk 422 optimal weight: 0.9990 chunk 628 optimal weight: 20.0000 chunk 417 optimal weight: 20.0000 chunk 744 optimal weight: 30.0000 chunk 465 optimal weight: 0.0040 chunk 453 optimal weight: 8.9990 chunk 343 optimal weight: 0.0770 overall best weight: 1.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN A1390 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN H 133 ASN H 139 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN Q 220 HIS ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 83 ASN d 119 ASN ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 165 ASN i 82 ASN ** k 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN n 173 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 775 ASN ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 528 HIS ** r 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 269 ASN r 277 ASN r 283 GLN r 294 GLN t 48 ASN ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4341 moved from start: 0.6516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 64249 Z= 0.208 Angle : 0.643 11.554 86727 Z= 0.336 Chirality : 0.044 0.235 9805 Planarity : 0.005 0.139 11160 Dihedral : 4.782 28.041 8482 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.88 % Rotamer: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.09), residues: 7715 helix: 0.94 (0.09), residues: 3346 sheet: -0.04 (0.15), residues: 1208 loop : -0.37 (0.11), residues: 3161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP q 279 HIS 0.007 0.001 HIS A1173 PHE 0.034 0.002 PHE a 18 TYR 0.038 0.002 TYR E 211 ARG 0.011 0.001 ARG d 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1314 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1311 time to evaluate : 5.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1314 average time/residue: 0.6464 time to fit residues: 1424.1436 Evaluate side-chains 1019 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1019 time to evaluate : 5.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 460 optimal weight: 0.0670 chunk 297 optimal weight: 9.9990 chunk 444 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 473 optimal weight: 50.0000 chunk 506 optimal weight: 9.9990 chunk 367 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 584 optimal weight: 6.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 969 GLN A1052 GLN A1187 GLN ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN H 131 ASN H 133 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN Q 220 HIS ** S 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN n 173 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 475 HIS ** n 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 3 GLN ** r 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 269 ASN ** r 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4679 moved from start: 0.7734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 64249 Z= 0.419 Angle : 0.884 15.677 86727 Z= 0.465 Chirality : 0.050 0.446 9805 Planarity : 0.007 0.169 11160 Dihedral : 5.597 29.325 8482 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 34.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.09), residues: 7715 helix: 0.11 (0.09), residues: 3339 sheet: -0.51 (0.15), residues: 1163 loop : -0.76 (0.11), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP h 125 HIS 0.013 0.002 HIS B1195 PHE 0.051 0.003 PHE d 81 TYR 0.047 0.003 TYR C 191 ARG 0.026 0.001 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1249 time to evaluate : 5.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 1250 average time/residue: 0.6492 time to fit residues: 1343.6055 Evaluate side-chains 1002 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1001 time to evaluate : 5.461 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5311 time to fit residues: 8.6795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 676 optimal weight: 10.0000 chunk 712 optimal weight: 0.4980 chunk 650 optimal weight: 5.9990 chunk 693 optimal weight: 0.9990 chunk 417 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 544 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 626 optimal weight: 30.0000 chunk 655 optimal weight: 0.5980 chunk 690 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 427 GLN A 439 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN A 723 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS ** A1354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN H 133 ASN I 12 ASN L 66 GLN ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 220 HIS ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 GLN h 42 GLN h 68 GLN ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 399 ASN ** q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 277 ASN ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4473 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 64249 Z= 0.214 Angle : 0.696 13.100 86727 Z= 0.363 Chirality : 0.046 0.316 9805 Planarity : 0.007 0.489 11160 Dihedral : 5.216 84.726 8482 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.09), residues: 7715 helix: 0.60 (0.09), residues: 3332 sheet: -0.39 (0.15), residues: 1214 loop : -0.56 (0.11), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP q 279 HIS 0.011 0.001 HIS B 744 PHE 0.049 0.002 PHE a 557 TYR 0.041 0.002 TYR H 115 ARG 0.020 0.001 ARG A1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1277 time to evaluate : 5.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1277 average time/residue: 0.6343 time to fit residues: 1350.0459 Evaluate side-chains 1011 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1011 time to evaluate : 5.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 455 optimal weight: 30.0000 chunk 733 optimal weight: 9.9990 chunk 447 optimal weight: 0.6980 chunk 347 optimal weight: 1.9990 chunk 509 optimal weight: 7.9990 chunk 769 optimal weight: 2.9990 chunk 707 optimal weight: 4.9990 chunk 612 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 473 optimal weight: 4.9990 chunk 375 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 439 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1354 ASN B 515 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN H 133 ASN ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 220 HIS ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 399 ASN ** n 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 701 ASN ** q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 269 ASN r 277 ASN r 294 GLN ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 46 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4567 moved from start: 0.8141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 64249 Z= 0.259 Angle : 0.722 13.639 86727 Z= 0.378 Chirality : 0.046 0.282 9805 Planarity : 0.006 0.167 11160 Dihedral : 5.192 43.101 8482 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.09), residues: 7715 helix: 0.51 (0.09), residues: 3335 sheet: -0.41 (0.15), residues: 1196 loop : -0.59 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP q 309 HIS 0.013 0.002 HIS k 51 PHE 0.046 0.002 PHE a 557 TYR 0.028 0.002 TYR E 211 ARG 0.030 0.001 ARG i 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15430 Ramachandran restraints generated. 7715 Oldfield, 0 Emsley, 7715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1241 time to evaluate : 6.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1241 average time/residue: 0.6429 time to fit residues: 1330.0119 Evaluate side-chains 999 residues out of total 7103 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 999 time to evaluate : 5.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 772 random chunks: chunk 486 optimal weight: 9.9990 chunk 652 optimal weight: 6.9990 chunk 187 optimal weight: 0.0070 chunk 564 optimal weight: 10.0000 chunk 90 optimal weight: 0.0670 chunk 170 optimal weight: 5.9990 chunk 613 optimal weight: 0.5980 chunk 256 optimal weight: 2.9990 chunk 629 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.8938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 439 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 ASN ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 GLN H 133 ASN ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 220 HIS ** S 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 144 GLN f 195 GLN ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** n 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 399 ASN ** n 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 277 ASN ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.182289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.126906 restraints weight = 251605.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.130430 restraints weight = 193192.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.135809 restraints weight = 146692.597| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4104 r_free = 0.4104 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4104 r_free = 0.4104 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.8167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 64249 Z= 0.194 Angle : 0.681 13.874 86727 Z= 0.354 Chirality : 0.046 0.261 9805 Planarity : 0.005 0.114 11160 Dihedral : 4.977 38.878 8482 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.10), residues: 7715 helix: 0.74 (0.09), residues: 3317 sheet: -0.25 (0.15), residues: 1184 loop : -0.49 (0.11), residues: 3214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 552 HIS 0.010 0.001 HIS B 744 PHE 0.043 0.002 PHE a 557 TYR 0.033 0.002 TYR A1349 ARG 0.037 0.001 ARG a 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20252.63 seconds wall clock time: 354 minutes 31.59 seconds (21271.59 seconds total)