Starting phenix.real_space_refine on Mon Dec 11 14:25:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/12_2023/7sl7_25193_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/12_2023/7sl7_25193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/12_2023/7sl7_25193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/12_2023/7sl7_25193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/12_2023/7sl7_25193_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl7_25193/12_2023/7sl7_25193_neut.pdb" } resolution = 3.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3460 atoms to isotropic. 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 124 5.16 5 C 9350 2.51 5 N 2524 2.21 5 O 2734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H GLU 21": "OE1" <-> "OE2" Residue "F TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14732 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "B" Number of atoms: 6623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6623 Classifications: {'peptide': 819} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 773} Chain breaks: 6 Chain: "G" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "H" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 214 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "I" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 200 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Time building chain proxies: 8.01, per 1000 atoms: 0.54 Number of scatterers: 14732 At special positions: 0 Unit cell: (120.35, 130.31, 173.47, 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 124 16.00 O 2734 8.00 N 2524 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 862 " distance=2.03 Simple disulfide: pdb=" SG CYS A 788 " - pdb=" SG CYS A 797 " distance=2.04 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS H 7 " - pdb=" SG CYS D 7 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS E 7 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS J 7 " - pdb=" SG CYS F 7 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 11 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 11 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 11 " distance=2.03 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: 5.38 Conformation dependent library (CDL) restraints added in 2.6 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 33 sheets defined 19.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.788A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.755A pdb=" N PHE A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.740A pdb=" N ILE A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.731A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.679A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.577A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.758A pdb=" N ALA A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.543A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.555A pdb=" N ARG A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 640 through 646 removed outlier: 4.002A pdb=" N LEU A 646 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 716 removed outlier: 3.659A pdb=" N ILE A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.839A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.741A pdb=" N PHE B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.746A pdb=" N ILE B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.730A pdb=" N ASP B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.584A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.727A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.569A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.558A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 640 through 646 removed outlier: 3.999A pdb=" N LEU B 646 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 716 removed outlier: 3.630A pdb=" N ILE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'G' and resid 8 through 19 Processing helix chain 'H' and resid 8 through 19 Processing helix chain 'I' and resid 8 through 19 Processing helix chain 'J' and resid 8 through 19 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 14 through 20 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 12 through 18 removed outlier: 3.688A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 13 through 18 removed outlier: 3.533A pdb=" N GLU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN E 18 " --> pdb=" O TYR E 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 13 through 18' Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 20 removed outlier: 3.758A pdb=" N GLU F 17 " --> pdb=" O TYR F 14 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN F 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 3.508A pdb=" N GLN A 34 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 36 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 121 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 5.549A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.625A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AB1, first strand: chain 'A' and resid 319 through 321 removed outlier: 7.687A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB3, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.628A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 601 through 606 removed outlier: 5.447A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 613 " --> pdb=" O ILE A 772 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 761 through 765 removed outlier: 3.759A pdb=" N VAL A 632 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 821 through 824 Processing sheet with id=AB8, first strand: chain 'A' and resid 859 through 864 removed outlier: 4.107A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 907 " --> pdb=" O GLY A 882 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 11 through 14 removed outlier: 3.509A pdb=" N GLN B 34 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 36 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 66 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 121 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC2, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC3, first strand: chain 'B' and resid 212 through 216 removed outlier: 5.566A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AC5, first strand: chain 'B' and resid 245 through 248 Processing sheet with id=AC6, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.570A pdb=" N THR B 302 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 321 removed outlier: 7.679A pdb=" N PHE B 427 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR B 401 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS B 429 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU B 403 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AD1, first strand: chain 'B' and resid 479 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.643A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.392A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 613 " --> pdb=" O ILE B 772 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 761 through 765 removed outlier: 3.808A pdb=" N VAL B 632 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD6, first strand: chain 'B' and resid 859 through 864 removed outlier: 3.511A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 907 " --> pdb=" O GLY B 882 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 966 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: 5.58 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4822 1.34 - 1.46: 3506 1.46 - 1.58: 6609 1.58 - 1.70: 1 1.70 - 1.82: 148 Bond restraints: 15086 Sorted by residual: bond pdb=" CB PRO B 720 " pdb=" CG PRO B 720 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.96e+00 bond pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.36e-02 5.41e+03 1.35e+00 bond pdb=" CA LEU A 305 " pdb=" C LEU A 305 " ideal model delta sigma weight residual 1.526 1.511 0.014 1.36e-02 5.41e+03 1.13e+00 bond pdb=" CB GLU B 6 " pdb=" CG GLU B 6 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.32e-01 bond pdb=" C GLN E 5 " pdb=" N CYS E 6 " ideal model delta sigma weight residual 1.332 1.345 -0.013 1.42e-02 4.96e+03 8.68e-01 ... (remaining 15081 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.13: 410 106.13 - 113.09: 7925 113.09 - 120.05: 5184 120.05 - 127.01: 6721 127.01 - 133.97: 200 Bond angle restraints: 20440 Sorted by residual: angle pdb=" C THR A 580 " pdb=" N TYR A 581 " pdb=" CA TYR A 581 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C THR B 580 " pdb=" N TYR B 581 " pdb=" CA TYR B 581 " ideal model delta sigma weight residual 121.54 131.92 -10.38 1.91e+00 2.74e-01 2.95e+01 angle pdb=" C GLU A 469 " pdb=" N ASN A 470 " pdb=" CA ASN A 470 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" C GLU B 469 " pdb=" N ASN B 470 " pdb=" CA ASN B 470 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N GLY I 8 " pdb=" CA GLY I 8 " pdb=" C GLY I 8 " ideal model delta sigma weight residual 111.35 115.50 -4.15 1.20e+00 6.94e-01 1.20e+01 ... (remaining 20435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 8212 16.10 - 32.21: 692 32.21 - 48.31: 174 48.31 - 64.41: 42 64.41 - 80.51: 26 Dihedral angle restraints: 9146 sinusoidal: 3816 harmonic: 5330 Sorted by residual: dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 170.92 -77.92 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 165.21 -72.21 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 6 " pdb=" SG CYS E 6 " pdb=" SG CYS E 11 " pdb=" CB CYS E 11 " ideal model delta sinusoidal sigma weight residual 93.00 39.14 53.86 1 1.00e+01 1.00e-02 3.94e+01 ... (remaining 9143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1464 0.036 - 0.072: 518 0.072 - 0.108: 153 0.108 - 0.144: 75 0.144 - 0.180: 6 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CB ILE A 174 " pdb=" CA ILE A 174 " pdb=" CG1 ILE A 174 " pdb=" CG2 ILE A 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CB ILE B 174 " pdb=" CA ILE B 174 " pdb=" CG1 ILE B 174 " pdb=" CG2 ILE B 174 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB THR B 690 " pdb=" CA THR B 690 " pdb=" OG1 THR B 690 " pdb=" CG2 THR B 690 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 2213 not shown) Planarity restraints: 2642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C THR B 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR B 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 580 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C THR A 580 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 580 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR A 581 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 836 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 837 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 837 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 837 " 0.024 5.00e-02 4.00e+02 ... (remaining 2639 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 358 2.70 - 3.25: 14045 3.25 - 3.80: 22611 3.80 - 4.35: 30781 4.35 - 4.90: 50028 Nonbonded interactions: 117823 Sorted by model distance: nonbonded pdb=" O ASP A 535 " pdb=" OH TYR E 14 " model vdw 2.149 2.440 nonbonded pdb=" O ASP B 535 " pdb=" OH TYR F 14 " model vdw 2.199 2.440 nonbonded pdb=" NH2 ARG A 889 " pdb=" OG1 THR A 891 " model vdw 2.241 2.520 nonbonded pdb=" NH2 ARG B 889 " pdb=" OG1 THR B 891 " model vdw 2.243 2.520 nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.266 2.440 ... (remaining 117818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'D' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'E' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ selection = (chain 'F' and (resid 1 through 2 or resid 4 through 12 or resid 14 through 21)) \ } ncs_group { reference = (chain 'G' and resid 2 through 26) selection = (chain 'H' and resid 2 through 26) selection = chain 'I' selection = chain 'J' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.980 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: 0.000 Extract box with map and model: 13.860 Check model and map are aligned: 0.030 Set scattering table: 0.140 Process input model: 41.970 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.002 0.099 15086 Z= 0.150 Angle : 0.565 10.495 20440 Z= 0.303 Chirality : 0.044 0.180 2216 Planarity : 0.003 0.044 2642 Dihedral : 13.076 80.513 5568 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.50 % Favored : 94.22 % Rotamer: Outliers : 0.24 % Allowed : 0.54 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.21), residues: 1782 helix: -0.31 (0.34), residues: 242 sheet: 0.45 (0.31), residues: 368 loop : -0.99 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 414 HIS 0.003 0.000 HIS I 5 PHE 0.021 0.001 PHE A 574 TYR 0.012 0.001 TYR A 507 ARG 0.007 0.000 ARG B 759 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 143 time to evaluate : 1.815 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 146 average time/residue: 0.2292 time to fit residues: 53.6216 Evaluate side-chains 102 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1329 time to fit residues: 2.7573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 867 HIS J 3 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15086 Z= 0.387 Angle : 0.651 7.728 20440 Z= 0.337 Chirality : 0.047 0.176 2216 Planarity : 0.004 0.044 2642 Dihedral : 4.959 26.704 1992 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.24 % Favored : 92.65 % Rotamer: Outliers : 1.08 % Allowed : 8.00 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.03 (0.21), residues: 1782 helix: -0.27 (0.33), residues: 258 sheet: 0.14 (0.29), residues: 376 loop : -1.09 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 412 HIS 0.010 0.001 HIS J 5 PHE 0.016 0.002 PHE B 567 TYR 0.024 0.002 TYR A 507 ARG 0.005 0.001 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.784 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 108 average time/residue: 0.2302 time to fit residues: 40.3943 Evaluate side-chains 101 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1391 time to fit residues: 5.0124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 0.1980 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 160 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN E 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15086 Z= 0.180 Angle : 0.533 5.743 20440 Z= 0.279 Chirality : 0.044 0.169 2216 Planarity : 0.003 0.046 2642 Dihedral : 4.680 29.657 1992 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.95 % Favored : 93.94 % Rotamer: Outliers : 0.36 % Allowed : 9.69 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.78 (0.21), residues: 1782 helix: 0.08 (0.34), residues: 246 sheet: 0.44 (0.30), residues: 352 loop : -0.98 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 899 HIS 0.003 0.001 HIS B 440 PHE 0.016 0.001 PHE A 574 TYR 0.017 0.001 TYR A 507 ARG 0.004 0.000 ARG B 889 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.930 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 108 average time/residue: 0.2204 time to fit residues: 39.3796 Evaluate side-chains 101 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1303 time to fit residues: 3.0742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN B 34 GLN B 90 ASN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 GLN J 3 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 15086 Z= 0.470 Angle : 0.684 6.614 20440 Z= 0.353 Chirality : 0.048 0.172 2216 Planarity : 0.004 0.045 2642 Dihedral : 5.331 26.216 1992 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.87 % Favored : 91.02 % Rotamer: Outliers : 1.62 % Allowed : 12.58 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.20 (0.20), residues: 1782 helix: -0.30 (0.33), residues: 254 sheet: -0.12 (0.28), residues: 380 loop : -1.19 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 899 HIS 0.008 0.001 HIS A 712 PHE 0.019 0.002 PHE A 567 TYR 0.024 0.002 TYR A 507 ARG 0.004 0.001 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.861 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 124 average time/residue: 0.2855 time to fit residues: 53.7218 Evaluate side-chains 102 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.800 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1451 time to fit residues: 5.7569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 70 optimal weight: 0.0470 chunk 146 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 154 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15086 Z= 0.163 Angle : 0.556 8.171 20440 Z= 0.290 Chirality : 0.044 0.267 2216 Planarity : 0.003 0.046 2642 Dihedral : 4.852 28.988 1992 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 0.90 % Allowed : 13.72 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.88 (0.21), residues: 1782 helix: 0.01 (0.33), residues: 248 sheet: 0.31 (0.30), residues: 348 loop : -1.04 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 899 HIS 0.002 0.001 HIS A 440 PHE 0.016 0.001 PHE A 707 TYR 0.017 0.001 TYR A 581 ARG 0.006 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.961 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 107 average time/residue: 0.2329 time to fit residues: 41.1821 Evaluate side-chains 96 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1834 time to fit residues: 4.3018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15086 Z= 0.260 Angle : 0.578 7.372 20440 Z= 0.300 Chirality : 0.045 0.219 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.928 28.871 1992 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.01 % Favored : 92.87 % Rotamer: Outliers : 0.72 % Allowed : 14.50 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.98 (0.21), residues: 1782 helix: -0.27 (0.32), residues: 272 sheet: 0.32 (0.29), residues: 348 loop : -1.09 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 412 HIS 0.005 0.001 HIS B 440 PHE 0.021 0.001 PHE B 574 TYR 0.020 0.001 TYR A 581 ARG 0.005 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.775 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 99 average time/residue: 0.2268 time to fit residues: 38.0160 Evaluate side-chains 96 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1436 time to fit residues: 3.8764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15086 Z= 0.195 Angle : 0.549 6.424 20440 Z= 0.287 Chirality : 0.044 0.187 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.792 31.757 1992 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.42 % Allowed : 15.10 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.84 (0.21), residues: 1782 helix: -0.09 (0.33), residues: 260 sheet: 0.41 (0.30), residues: 338 loop : -0.99 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 899 HIS 0.006 0.001 HIS A 712 PHE 0.021 0.001 PHE B 574 TYR 0.020 0.001 TYR B 492 ARG 0.005 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.880 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 101 average time/residue: 0.2310 time to fit residues: 38.7374 Evaluate side-chains 92 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1356 time to fit residues: 2.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 0.0060 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15086 Z= 0.196 Angle : 0.545 6.631 20440 Z= 0.286 Chirality : 0.044 0.209 2216 Planarity : 0.003 0.044 2642 Dihedral : 4.720 34.365 1992 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.60 % Allowed : 15.22 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.80 (0.21), residues: 1782 helix: -0.04 (0.33), residues: 260 sheet: 0.47 (0.30), residues: 338 loop : -0.98 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 899 HIS 0.006 0.001 HIS A 712 PHE 0.016 0.001 PHE A 574 TYR 0.020 0.001 TYR B 492 ARG 0.004 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 2.310 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 103 average time/residue: 0.2408 time to fit residues: 40.9307 Evaluate side-chains 95 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1300 time to fit residues: 3.0127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15086 Z= 0.247 Angle : 0.571 6.436 20440 Z= 0.298 Chirality : 0.045 0.221 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.878 30.574 1992 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.24 % Allowed : 15.70 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.87 (0.21), residues: 1782 helix: -0.19 (0.32), residues: 272 sheet: 0.50 (0.30), residues: 338 loop : -1.04 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 899 HIS 0.006 0.001 HIS A 712 PHE 0.016 0.001 PHE A 574 TYR 0.020 0.001 TYR B 581 ARG 0.004 0.000 ARG B 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.960 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 0.2480 time to fit residues: 40.5949 Evaluate side-chains 93 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.974 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1330 time to fit residues: 3.3711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15086 Z= 0.198 Angle : 0.556 8.692 20440 Z= 0.291 Chirality : 0.044 0.214 2216 Planarity : 0.003 0.045 2642 Dihedral : 4.736 28.407 1992 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.36 % Allowed : 15.94 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.81 (0.21), residues: 1782 helix: -0.04 (0.33), residues: 260 sheet: 0.41 (0.30), residues: 342 loop : -0.97 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 899 HIS 0.005 0.001 HIS A 712 PHE 0.015 0.001 PHE A 574 TYR 0.016 0.001 TYR B 581 ARG 0.004 0.000 ARG A 658 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.925 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 0.2444 time to fit residues: 41.0339 Evaluate side-chains 98 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1380 time to fit residues: 3.1248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.8528 > 50: distance: 71 - 91: 28.006 distance: 74 - 88: 19.885 distance: 82 - 88: 20.235 distance: 88 - 89: 39.699 distance: 89 - 90: 45.246 distance: 89 - 92: 46.957 distance: 90 - 91: 52.288 distance: 90 - 97: 29.666 distance: 92 - 93: 44.946 distance: 93 - 94: 23.823 distance: 94 - 95: 54.028 distance: 95 - 96: 48.820 distance: 97 - 98: 35.527 distance: 98 - 99: 21.682 distance: 98 - 101: 41.487 distance: 99 - 100: 33.176 distance: 99 - 111: 25.780 distance: 101 - 102: 26.880 distance: 102 - 103: 4.875 distance: 102 - 104: 4.541 distance: 103 - 105: 6.216 distance: 104 - 106: 5.332 distance: 104 - 107: 3.161 distance: 105 - 106: 3.913 distance: 106 - 108: 4.310 distance: 107 - 109: 4.125 distance: 109 - 110: 3.976 distance: 111 - 112: 28.373 distance: 112 - 113: 24.717 distance: 112 - 115: 23.238 distance: 113 - 114: 46.420 distance: 113 - 120: 25.108 distance: 115 - 116: 58.618 distance: 116 - 117: 46.091 distance: 117 - 118: 48.603 distance: 118 - 119: 40.756 distance: 120 - 121: 43.323 distance: 120 - 126: 19.722 distance: 121 - 122: 35.071 distance: 121 - 124: 43.206 distance: 122 - 123: 20.312 distance: 122 - 127: 32.756 distance: 124 - 125: 56.541 distance: 125 - 126: 47.842 distance: 127 - 128: 15.583 distance: 127 - 133: 38.100 distance: 128 - 129: 15.194 distance: 128 - 131: 24.962 distance: 129 - 130: 19.119 distance: 129 - 134: 46.129 distance: 131 - 132: 26.084 distance: 132 - 133: 19.662 distance: 134 - 135: 39.151 distance: 135 - 136: 45.032 distance: 135 - 138: 20.999 distance: 136 - 137: 48.622 distance: 136 - 140: 62.298 distance: 138 - 139: 38.072 distance: 140 - 141: 52.646 distance: 141 - 142: 27.577 distance: 141 - 144: 21.160 distance: 142 - 143: 40.242 distance: 142 - 148: 24.927 distance: 144 - 145: 43.915 distance: 145 - 146: 62.082 distance: 145 - 147: 44.003 distance: 148 - 149: 15.509 distance: 148 - 154: 44.601 distance: 149 - 150: 25.311 distance: 149 - 152: 33.534 distance: 150 - 151: 34.339 distance: 150 - 155: 34.351 distance: 152 - 153: 17.750 distance: 153 - 154: 37.857 distance: 155 - 156: 40.162 distance: 156 - 157: 36.039 distance: 156 - 159: 33.097 distance: 157 - 158: 49.519 distance: 157 - 163: 42.789 distance: 159 - 160: 11.446 distance: 160 - 161: 48.952 distance: 160 - 162: 60.057 distance: 163 - 164: 33.077 distance: 164 - 165: 21.506 distance: 165 - 166: 23.223 distance: 165 - 167: 5.317