Starting phenix.real_space_refine on Thu Feb 22 08:59:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7d_30605/02_2024/7d7d_30605.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7d_30605/02_2024/7d7d_30605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7d_30605/02_2024/7d7d_30605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7d_30605/02_2024/7d7d_30605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7d_30605/02_2024/7d7d_30605.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d7d_30605/02_2024/7d7d_30605.pdb" } resolution = 4.5 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= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 94 5.49 5 Mg 1 5.21 5 S 132 5.16 5 C 20949 2.51 5 N 5888 2.21 5 O 6689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 516": "OD1" <-> "OD2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 610": "OE1" <-> "OE2" Residue "C TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 781": "OD1" <-> "OD2" Residue "C ASP 790": "OD1" <-> "OD2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C GLU 867": "OE1" <-> "OE2" Residue "C TYR 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 881": "OD1" <-> "OD2" Residue "C ASP 930": "OD1" <-> "OD2" Residue "C ASP 937": "OD1" <-> "OD2" Residue "C ASP 942": "OD1" <-> "OD2" Residue "C GLU 962": "OE1" <-> "OE2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C ASP 1019": "OD1" <-> "OD2" Residue "C PHE 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1064": "OD1" <-> "OD2" Residue "C TYR 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1321": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 622": "OD1" <-> "OD2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 643": "OD1" <-> "OD2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 751": "OD1" <-> "OD2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D ASP 812": "OD1" <-> "OD2" Residue "D ASP 889": "OD1" <-> "OD2" Residue "D PHE 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1015": "OE1" <-> "OE2" Residue "D PHE 1034": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1042": "OD1" <-> "OD2" Residue "D ASP 1063": "OD1" <-> "OD2" Residue "D TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1143": "OD1" <-> "OD2" Residue "D ASP 1181": "OD1" <-> "OD2" Residue "D TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 74": "OD1" <-> "OD2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 91": "OD1" <-> "OD2" Residue "E PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 36": "OD1" <-> "OD2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "G ASP 6": "OD1" <-> "OD2" Residue "G PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 70": "OD1" <-> "OD2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 96": "OD1" <-> "OD2" Residue "G PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 223": "OD1" <-> "OD2" Residue "G ASP 227": "OD1" <-> "OD2" Residue "H ASP 49": "OD1" <-> "OD2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "H PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 156": "OE1" <-> "OE2" Residue "I TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 173": "OD1" <-> "OD2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33755 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1686 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10384 Classifications: {'peptide': 1335} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1279} Chain breaks: 2 Chain: "T" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 939 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "F" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1128 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 1 Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 990 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "K" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 558 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 564 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "G" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "I" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14537 SG CYS D 88 113.469 68.577 73.984 1.00202.45 S ATOM 20225 SG CYS D 814 85.986 82.912 136.182 1.00122.90 S ATOM 20790 SG CYS D 888 85.868 82.918 132.318 1.00119.14 S ATOM 20841 SG CYS D 895 84.420 80.053 134.163 1.00112.38 S ATOM 20862 SG CYS D 898 82.965 83.085 134.219 1.00109.26 S Time building chain proxies: 17.57, per 1000 atoms: 0.52 Number of scatterers: 33755 At special positions: 0 Unit cell: (167.296, 177.752, 169.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 132 16.00 P 94 15.00 Mg 1 11.99 O 6689 8.00 N 5888 7.00 C 20949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 16.06 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " Number of angles added : 6 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7554 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 55 sheets defined 35.7% alpha, 16.4% beta 38 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 11.97 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.938A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.152A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.670A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.588A pdb=" N ARG C 245 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.703A pdb=" N SER C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.289A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.561A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.704A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 4.440A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 526 Processing helix chain 'C' and resid 551 through 555 Processing helix chain 'C' and resid 609 through 614 removed outlier: 3.738A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.644A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 Processing helix chain 'C' and resid 858 through 865 removed outlier: 4.111A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.604A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 969 removed outlier: 3.934A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 981 removed outlier: 4.349A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.268A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1123 Processing helix chain 'C' and resid 1124 through 1134 removed outlier: 3.621A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.071A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 4.174A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 4.186A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.680A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.725A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 194 through 208 Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.680A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.733A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 284 removed outlier: 3.638A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.571A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.682A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.997A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.576A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.664A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.502A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 4.221A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.694A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.662A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1226 through 1243 Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.507A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1293 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1325 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.994A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1351 removed outlier: 3.583A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 3.862A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 28 removed outlier: 3.526A pdb=" N LEU F 16 " --> pdb=" O ASN F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 56 removed outlier: 3.608A pdb=" N LYS F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 83 removed outlier: 3.564A pdb=" N GLU F 70 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 126 removed outlier: 3.718A pdb=" N HIS F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.708A pdb=" N ASP F 141 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR F 153 " --> pdb=" O TYR F 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 51 removed outlier: 3.570A pdb=" N LYS K 46 " --> pdb=" O PHE K 42 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 48 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 66 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.659A pdb=" N LYS K 84 " --> pdb=" O GLY K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 101 removed outlier: 3.563A pdb=" N VAL K 100 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 96 through 101' Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.558A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 60 through 72 Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 96 through 100 Processing helix chain 'G' and resid 119 through 133 removed outlier: 3.821A pdb=" N ARG G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 157 Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'H' and resid 4 through 18 removed outlier: 3.924A pdb=" N ILE H 17 " --> pdb=" O ASN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 67 Processing helix chain 'H' and resid 119 through 134 removed outlier: 4.590A pdb=" N ARG H 131 " --> pdb=" O LEU H 127 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 16 removed outlier: 3.642A pdb=" N THR I 16 " --> pdb=" O LYS I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 67 removed outlier: 4.242A pdb=" N VAL I 67 " --> pdb=" O ILE I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 100 removed outlier: 3.560A pdb=" N VAL I 100 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 133 removed outlier: 3.559A pdb=" N ARG I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 187 No H-bonds generated for 'chain 'I' and resid 185 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 6.501A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 3.822A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.563A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 4.039A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.736A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.102A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.326A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.134A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C 119 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 102 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 117 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.825A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB6, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB7, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.724A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AB9, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.535A pdb=" N ALA C 257 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC2, first strand: chain 'C' and resid 599 through 605 removed outlier: 5.595A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 637 " --> pdb=" O ILE C 616 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.600A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 748 through 751 removed outlier: 6.337A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 4.358A pdb=" N LYS C1065 " --> pdb=" O LEU C1235 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C1068 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN C1072 " --> pdb=" O GLY C1068 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 838 removed outlier: 3.507A pdb=" N GLN C 834 " --> pdb=" O LEU C1054 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.653A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'C' and resid 1337 through 1339 Processing sheet with id=AD4, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.361A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.822A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD6, first strand: chain 'D' and resid 317 through 319 removed outlier: 6.097A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.352A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.161A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.370A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 959 Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.630A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1050 Processing sheet with id=AE6, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.918A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.869A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.484A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 21 through 23 Processing sheet with id=AF1, first strand: chain 'G' and resid 26 through 32 removed outlier: 4.975A pdb=" N GLN G 27 " --> pdb=" O ILE G 44 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 72 through 75 Processing sheet with id=AF3, first strand: chain 'G' and resid 165 through 171 removed outlier: 3.513A pdb=" N TYR G 165 " --> pdb=" O GLY G 151 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE G 147 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL G 142 " --> pdb=" O PHE G 178 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE G 178 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN G 179 " --> pdb=" O ASP G 223 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP G 223 " --> pdb=" O ASN G 179 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE G 181 " --> pdb=" O GLU G 221 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AF5, first strand: chain 'H' and resid 26 through 32 removed outlier: 4.111A pdb=" N PHE H 28 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ASP H 46 " --> pdb=" O PHE H 28 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N MET H 30 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 10.935A pdb=" N ILE H 44 " --> pdb=" O MET H 30 " (cutoff:3.500A) removed outlier: 11.700A pdb=" N ARG H 32 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N ALA H 42 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 72 through 75 Processing sheet with id=AF7, first strand: chain 'H' and resid 225 through 226 removed outlier: 5.846A pdb=" N PHE H 178 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE H 147 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU H 169 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR H 165 " --> pdb=" O GLY H 151 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS H 164 " --> pdb=" O PHE I 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 21 through 23 Processing sheet with id=AF9, first strand: chain 'I' and resid 26 through 32 removed outlier: 5.195A pdb=" N GLN I 27 " --> pdb=" O ILE I 44 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA I 214 " --> pdb=" O GLY I 211 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 166 through 171 removed outlier: 6.467A pdb=" N ILE I 147 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL I 142 " --> pdb=" O PHE I 178 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE I 178 " --> pdb=" O VAL I 142 " (cutoff:3.500A) 1329 hydrogen bonds defined for protein. 3642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 16.92 Time building geometry restraints manager: 16.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8717 1.33 - 1.45: 6333 1.45 - 1.57: 18998 1.57 - 1.69: 185 1.69 - 1.81: 234 Bond restraints: 34467 Sorted by residual: bond pdb=" CA LEU C 448 " pdb=" C LEU C 448 " ideal model delta sigma weight residual 1.522 1.433 0.088 1.45e-02 4.76e+03 3.71e+01 bond pdb=" CA GLN C 658 " pdb=" C GLN C 658 " ideal model delta sigma weight residual 1.523 1.452 0.072 1.34e-02 5.57e+03 2.85e+01 bond pdb=" CA GLN C 659 " pdb=" C GLN C 659 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.34e-02 5.57e+03 2.51e+01 bond pdb=" C CYS C 559 " pdb=" N PRO C 560 " ideal model delta sigma weight residual 1.336 1.280 0.055 1.23e-02 6.61e+03 2.03e+01 bond pdb=" CA LYS C 163 " pdb=" C LYS C 163 " ideal model delta sigma weight residual 1.523 1.471 0.053 1.34e-02 5.57e+03 1.54e+01 ... (remaining 34462 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.16: 794 104.16 - 111.64: 16421 111.64 - 119.13: 12162 119.13 - 126.61: 17053 126.61 - 134.10: 543 Bond angle restraints: 46973 Sorted by residual: angle pdb=" CA ARG C 821 " pdb=" C ARG C 821 " pdb=" N VAL C 822 " ideal model delta sigma weight residual 118.43 124.40 -5.97 1.33e+00 5.65e-01 2.01e+01 angle pdb=" C GLY B 209 " pdb=" N THR B 210 " pdb=" CA THR B 210 " ideal model delta sigma weight residual 122.38 114.49 7.89 1.81e+00 3.05e-01 1.90e+01 angle pdb=" N HIS D 430 " pdb=" CA HIS D 430 " pdb=" C HIS D 430 " ideal model delta sigma weight residual 108.34 113.86 -5.52 1.31e+00 5.83e-01 1.78e+01 angle pdb=" C ILE A 211 " pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 120.69 109.24 11.45 2.95e+00 1.15e-01 1.51e+01 angle pdb=" N GLY C1045 " pdb=" CA GLY C1045 " pdb=" C GLY C1045 " ideal model delta sigma weight residual 114.85 109.76 5.09 1.35e+00 5.49e-01 1.42e+01 ... (remaining 46968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.80: 18949 23.80 - 47.60: 1559 47.60 - 71.40: 323 71.40 - 95.20: 43 95.20 - 118.99: 2 Dihedral angle restraints: 20876 sinusoidal: 9149 harmonic: 11727 Sorted by residual: dihedral pdb=" CA ARG D1149 " pdb=" C ARG D1149 " pdb=" N PRO D1150 " pdb=" CA PRO D1150 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N GLU B 76 " pdb=" CA GLU B 76 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ALA C 746 " pdb=" C ALA C 746 " pdb=" N GLY C 747 " pdb=" CA GLY C 747 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 20873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4328 0.062 - 0.123: 961 0.123 - 0.185: 80 0.185 - 0.246: 6 0.246 - 0.308: 1 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CB ILE G 83 " pdb=" CA ILE G 83 " pdb=" CG1 ILE G 83 " pdb=" CG2 ILE G 83 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ILE C1079 " pdb=" N ILE C1079 " pdb=" C ILE C1079 " pdb=" CB ILE C1079 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG D 764 " pdb=" N ARG D 764 " pdb=" C ARG D 764 " pdb=" CB ARG D 764 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5373 not shown) Planarity restraints: 5798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C1080 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO C1081 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C1081 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO C1081 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 858 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO D 859 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 859 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 859 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 28 " 0.015 2.00e-02 2.50e+03 1.54e-02 5.34e+00 pdb=" N1 DC T 28 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC T 28 " -0.030 2.00e-02 2.50e+03 pdb=" O2 DC T 28 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DC T 28 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DC T 28 " -0.015 2.00e-02 2.50e+03 pdb=" N4 DC T 28 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DC T 28 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC T 28 " 0.008 2.00e-02 2.50e+03 ... (remaining 5795 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 684 2.56 - 3.15: 32904 3.15 - 3.73: 55862 3.73 - 4.32: 76306 4.32 - 4.90: 115470 Nonbonded interactions: 281226 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR K 71 " pdb=" OE1 GLN K 72 " model vdw 2.100 2.440 nonbonded pdb=" NZ LYS B 104 " pdb=" O SER B 105 " model vdw 2.107 2.520 nonbonded pdb=" N GLU B 80 " pdb=" OE1 GLU B 80 " model vdw 2.177 2.520 nonbonded pdb=" N GLU D 913 " pdb=" OE1 GLU D 913 " model vdw 2.180 2.520 ... (remaining 281221 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' and (resid 8 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 158 or resid 170 through 232)) selection = (chain 'B' and (resid 8 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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 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: 0.840 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: 0.020 Extract box with map and model: 5.570 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 110.520 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.160 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 : 0.008 0.102 34467 Z= 0.527 Angle : 0.931 11.900 46973 Z= 0.530 Chirality : 0.049 0.308 5376 Planarity : 0.005 0.110 5798 Dihedral : 17.660 118.994 13322 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 34.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.62 % Favored : 84.31 % Rotamer: Outliers : 0.67 % Allowed : 11.74 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -5.01 (0.10), residues: 4046 helix: -3.24 (0.10), residues: 1320 sheet: -2.52 (0.20), residues: 523 loop : -3.70 (0.10), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 183 HIS 0.010 0.002 HIS D1227 PHE 0.018 0.002 PHE C 224 TYR 0.025 0.003 TYR G 55 ARG 0.010 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 658 time to evaluate : 3.579 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: A 23 HIS cc_start: 0.5651 (p-80) cc_final: 0.5222 (p90) REVERT: A 123 ILE cc_start: 0.9117 (mm) cc_final: 0.8819 (mt) REVERT: A 223 ILE cc_start: 0.9639 (mt) cc_final: 0.9237 (mm) REVERT: A 226 GLU cc_start: 0.8829 (tt0) cc_final: 0.8345 (mt-10) REVERT: B 10 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8379 (mppt) REVERT: B 214 GLU cc_start: 0.8101 (tt0) cc_final: 0.7862 (tt0) REVERT: C 151 ARG cc_start: 0.8123 (mtp180) cc_final: 0.7261 (mtm110) REVERT: C 185 ASP cc_start: 0.7484 (t0) cc_final: 0.7239 (t0) REVERT: C 322 LEU cc_start: 0.9394 (tt) cc_final: 0.9123 (mt) REVERT: C 434 ASP cc_start: 0.9246 (m-30) cc_final: 0.8967 (m-30) REVERT: C 473 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7601 (mmt180) REVERT: C 488 MET cc_start: 0.8818 (mmm) cc_final: 0.8444 (mmm) REVERT: C 515 MET cc_start: 0.7140 (ttt) cc_final: 0.6470 (ttt) REVERT: C 522 SER cc_start: 0.7572 (p) cc_final: 0.7108 (p) REVERT: C 685 MET cc_start: 0.6844 (mtm) cc_final: 0.6038 (mtt) REVERT: C 752 ASN cc_start: 0.8785 (m-40) cc_final: 0.8383 (t0) REVERT: C 768 MET cc_start: 0.7616 (mtm) cc_final: 0.6752 (ptt) REVERT: C 800 MET cc_start: 0.7791 (mtt) cc_final: 0.7467 (mmm) REVERT: C 807 TRP cc_start: 0.8430 (OUTLIER) cc_final: 0.7817 (t60) REVERT: C 817 LEU cc_start: 0.8551 (tp) cc_final: 0.8324 (tp) REVERT: C 835 GLU cc_start: 0.8145 (tt0) cc_final: 0.7460 (pp20) REVERT: C 844 LYS cc_start: 0.7639 (ptpt) cc_final: 0.7250 (ptmt) REVERT: C 853 ASP cc_start: 0.7731 (t70) cc_final: 0.7229 (t70) REVERT: C 878 THR cc_start: 0.6693 (p) cc_final: 0.6394 (t) REVERT: C 906 PHE cc_start: 0.8925 (m-80) cc_final: 0.8719 (m-80) REVERT: C 1197 GLU cc_start: 0.8739 (tp30) cc_final: 0.8531 (mt-10) REVERT: C 1230 MET cc_start: 0.5762 (ttm) cc_final: 0.4763 (ptm) REVERT: C 1235 LEU cc_start: 0.7700 (tp) cc_final: 0.7499 (mp) REVERT: C 1243 MET cc_start: 0.7228 (ttp) cc_final: 0.6939 (ttt) REVERT: C 1244 HIS cc_start: 0.7766 (t70) cc_final: 0.7433 (t70) REVERT: C 1272 GLU cc_start: 0.6812 (pm20) cc_final: 0.6402 (pt0) REVERT: C 1276 TRP cc_start: 0.8465 (m-10) cc_final: 0.7520 (m-90) REVERT: D 45 ASN cc_start: 0.8327 (t0) cc_final: 0.7858 (t0) REVERT: D 111 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8749 (m) REVERT: D 164 GLN cc_start: 0.9288 (mt0) cc_final: 0.9039 (mt0) REVERT: D 222 LYS cc_start: 0.9575 (ttpt) cc_final: 0.9100 (tptp) REVERT: D 227 PHE cc_start: 0.9057 (m-80) cc_final: 0.8693 (m-80) REVERT: D 244 VAL cc_start: 0.8060 (m) cc_final: 0.7791 (m) REVERT: D 248 ASP cc_start: 0.7575 (m-30) cc_final: 0.7198 (t0) REVERT: D 334 LYS cc_start: 0.8288 (ptpt) cc_final: 0.8007 (ptpp) REVERT: D 339 ARG cc_start: 0.6663 (mtp180) cc_final: 0.6017 (mtp85) REVERT: D 402 GLU cc_start: 0.7808 (tp30) cc_final: 0.7602 (mm-30) REVERT: D 404 GLU cc_start: 0.7219 (pm20) cc_final: 0.6860 (pp20) REVERT: D 405 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7129 (mp0) REVERT: D 466 MET cc_start: 0.8892 (mtp) cc_final: 0.8617 (mtp) REVERT: D 478 LEU cc_start: 0.8871 (mt) cc_final: 0.8564 (mt) REVERT: D 479 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7856 (mt-10) REVERT: D 484 MET cc_start: 0.7120 (mpp) cc_final: 0.6762 (mpp) REVERT: D 485 MET cc_start: 0.6804 (tpt) cc_final: 0.6333 (ttp) REVERT: D 501 VAL cc_start: 0.7561 (p) cc_final: 0.7211 (m) REVERT: D 697 MET cc_start: 0.7911 (tmm) cc_final: 0.7654 (tmm) REVERT: D 710 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: D 714 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7520 (mp0) REVERT: D 743 MET cc_start: 0.7385 (ptm) cc_final: 0.7046 (ptp) REVERT: D 795 TYR cc_start: 0.8382 (t80) cc_final: 0.8001 (t80) REVERT: D 864 LEU cc_start: 0.9104 (mt) cc_final: 0.8888 (mt) REVERT: D 925 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8636 (tm-30) REVERT: D 1349 GLU cc_start: 0.7035 (pt0) cc_final: 0.6688 (pm20) REVERT: D 1370 MET cc_start: 0.7872 (tpt) cc_final: 0.7657 (tpt) REVERT: F 113 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7528 (tp30) REVERT: F 116 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8774 (tm-30) REVERT: K 40 ASN cc_start: 0.9436 (t0) cc_final: 0.9110 (t0) REVERT: K 47 MET cc_start: 0.8772 (mmm) cc_final: 0.8461 (mmm) REVERT: K 55 TYR cc_start: 0.8844 (m-80) cc_final: 0.7981 (m-80) REVERT: K 85 ILE cc_start: 0.9256 (mm) cc_final: 0.8919 (mm) REVERT: K 86 GLN cc_start: 0.9186 (mt0) cc_final: 0.8907 (mt0) REVERT: E 30 MET cc_start: 0.8124 (mtm) cc_final: 0.7819 (mtm) REVERT: G 183 ASN cc_start: 0.9212 (t0) cc_final: 0.8966 (m-40) REVERT: G 184 MET cc_start: 0.7915 (mmm) cc_final: 0.7542 (mmm) REVERT: H 187 MET cc_start: 0.7099 (mmm) cc_final: 0.6741 (mpp) REVERT: I 165 TYR cc_start: 0.9116 (t80) cc_final: 0.8690 (t80) REVERT: I 187 MET cc_start: 0.8241 (mtp) cc_final: 0.7539 (ptm) outliers start: 23 outliers final: 12 residues processed: 679 average time/residue: 0.5490 time to fit residues: 576.5918 Evaluate side-chains 420 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 405 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 346 optimal weight: 30.0000 chunk 310 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 209 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 321 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 372 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 66 HIS A 84 ASN A 93 GLN A 147 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 66 HIS C 65 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 618 GLN C 684 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN C1116 HIS C1134 GLN ** C1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 341 ASN D 365 GLN D 419 HIS D 430 HIS D 465 GLN D 489 ASN D 739 GLN D1023 HIS ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1326 GLN ** F 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN K 66 ASN K 86 GLN E 43 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN I 186 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34467 Z= 0.236 Angle : 0.680 10.305 46973 Z= 0.362 Chirality : 0.045 0.229 5376 Planarity : 0.005 0.064 5798 Dihedral : 16.839 128.006 5465 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.39 % Favored : 92.59 % Rotamer: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -3.19 (0.12), residues: 4046 helix: -1.23 (0.13), residues: 1333 sheet: -1.92 (0.20), residues: 520 loop : -2.84 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 23 HIS 0.007 0.001 HIS A 66 PHE 0.016 0.002 PHE H 28 TYR 0.026 0.002 TYR C1231 ARG 0.006 0.001 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 579 time to evaluate : 4.142 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: A 226 GLU cc_start: 0.8700 (tt0) cc_final: 0.8227 (tt0) REVERT: B 10 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8063 (tmtt) REVERT: C 26 TYR cc_start: 0.8199 (t80) cc_final: 0.7330 (t80) REVERT: C 84 GLU cc_start: 0.7730 (mp0) cc_final: 0.7257 (mp0) REVERT: C 105 TYR cc_start: 0.9005 (m-10) cc_final: 0.8698 (m-80) REVERT: C 151 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7188 (mtm110) REVERT: C 185 ASP cc_start: 0.7968 (t0) cc_final: 0.7339 (t0) REVERT: C 394 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7883 (mmt180) REVERT: C 443 ASP cc_start: 0.9209 (m-30) cc_final: 0.9007 (m-30) REVERT: C 488 MET cc_start: 0.8640 (mmm) cc_final: 0.8363 (mmm) REVERT: C 504 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8210 (tm-30) REVERT: C 515 MET cc_start: 0.6626 (ttt) cc_final: 0.6224 (ttt) REVERT: C 685 MET cc_start: 0.6605 (mtm) cc_final: 0.6114 (mtt) REVERT: C 728 ASP cc_start: 0.9077 (t0) cc_final: 0.8746 (t70) REVERT: C 768 MET cc_start: 0.7894 (mtm) cc_final: 0.6955 (ptt) REVERT: C 835 GLU cc_start: 0.8046 (tt0) cc_final: 0.7138 (pp20) REVERT: C 878 THR cc_start: 0.6829 (p) cc_final: 0.6462 (t) REVERT: C 881 ASP cc_start: 0.7909 (t70) cc_final: 0.7560 (t70) REVERT: C 1020 GLU cc_start: 0.9183 (tt0) cc_final: 0.8702 (pt0) REVERT: C 1119 MET cc_start: 0.8339 (tpp) cc_final: 0.7882 (tpp) REVERT: C 1230 MET cc_start: 0.6106 (ttm) cc_final: 0.5458 (ptm) REVERT: C 1232 MET cc_start: 0.8030 (mmm) cc_final: 0.7252 (mtp) REVERT: C 1235 LEU cc_start: 0.7563 (tp) cc_final: 0.7354 (mp) REVERT: C 1276 TRP cc_start: 0.8565 (m-10) cc_final: 0.7721 (m-90) REVERT: C 1290 MET cc_start: 0.7185 (tpp) cc_final: 0.6788 (tpp) REVERT: D 136 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8589 (tp30) REVERT: D 160 LEU cc_start: 0.9069 (mm) cc_final: 0.8662 (mm) REVERT: D 164 GLN cc_start: 0.9166 (mt0) cc_final: 0.8806 (mt0) REVERT: D 201 LEU cc_start: 0.8991 (mt) cc_final: 0.8283 (tt) REVERT: D 227 PHE cc_start: 0.8868 (m-80) cc_final: 0.8651 (m-80) REVERT: D 248 ASP cc_start: 0.7679 (m-30) cc_final: 0.7329 (t0) REVERT: D 284 ASP cc_start: 0.9083 (m-30) cc_final: 0.8792 (m-30) REVERT: D 334 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7977 (ptpp) REVERT: D 345 LYS cc_start: 0.7131 (ptmt) cc_final: 0.6873 (ptpp) REVERT: D 398 LYS cc_start: 0.8559 (mttt) cc_final: 0.8033 (tptp) REVERT: D 478 LEU cc_start: 0.8427 (mt) cc_final: 0.8004 (mt) REVERT: D 479 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7306 (mt-10) REVERT: D 484 MET cc_start: 0.7617 (mpp) cc_final: 0.7084 (mpp) REVERT: D 555 TYR cc_start: 0.8434 (m-10) cc_final: 0.8179 (m-10) REVERT: D 569 LEU cc_start: 0.8977 (tp) cc_final: 0.8764 (mp) REVERT: D 571 ASP cc_start: 0.8379 (t0) cc_final: 0.8140 (t0) REVERT: D 714 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7558 (mp0) REVERT: D 743 MET cc_start: 0.7570 (ptm) cc_final: 0.7241 (ptp) REVERT: D 811 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8449 (tm-30) REVERT: D 925 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8549 (tt0) REVERT: D 1219 ASP cc_start: 0.8949 (t70) cc_final: 0.8697 (t0) REVERT: D 1345 ARG cc_start: 0.6906 (mmt90) cc_final: 0.6597 (mmt90) REVERT: F 52 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8038 (mm-30) REVERT: F 74 ASP cc_start: 0.9040 (t0) cc_final: 0.8818 (t0) REVERT: F 136 MET cc_start: 0.6931 (tpp) cc_final: 0.6547 (tpp) REVERT: K 55 TYR cc_start: 0.8897 (m-80) cc_final: 0.8582 (m-80) REVERT: K 86 GLN cc_start: 0.9227 (mt0) cc_final: 0.8931 (mt0) REVERT: K 93 ASN cc_start: 0.8699 (t0) cc_final: 0.8469 (t0) REVERT: E 11 GLU cc_start: 0.6476 (mm-30) cc_final: 0.6226 (mm-30) REVERT: E 30 MET cc_start: 0.8496 (mtm) cc_final: 0.8266 (mtp) REVERT: E 59 ILE cc_start: 0.7937 (tt) cc_final: 0.7503 (tt) REVERT: E 60 ASN cc_start: 0.7833 (p0) cc_final: 0.7510 (p0) REVERT: E 63 ILE cc_start: 0.9171 (mm) cc_final: 0.8932 (mm) REVERT: E 64 LEU cc_start: 0.9174 (tt) cc_final: 0.8915 (pp) REVERT: E 67 ARG cc_start: 0.9137 (ttp-110) cc_final: 0.8641 (mtm-85) REVERT: G 183 ASN cc_start: 0.9078 (t0) cc_final: 0.8839 (t0) REVERT: I 1 MET cc_start: 0.7235 (ttm) cc_final: 0.6900 (ttt) REVERT: I 189 MET cc_start: 0.4882 (ptp) cc_final: 0.4389 (ptp) outliers start: 5 outliers final: 0 residues processed: 582 average time/residue: 0.5309 time to fit residues: 492.3532 Evaluate side-chains 391 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 206 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 372 optimal weight: 50.0000 chunk 402 optimal weight: 20.0000 chunk 332 optimal weight: 5.9990 chunk 369 optimal weight: 50.0000 chunk 127 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 84 ASN A 93 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 952 GLN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 489 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 HIS ** F 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 34467 Z= 0.339 Angle : 0.711 10.189 46973 Z= 0.376 Chirality : 0.046 0.263 5376 Planarity : 0.005 0.136 5798 Dihedral : 16.621 128.855 5465 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.54 % Favored : 90.43 % Rotamer: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -2.70 (0.12), residues: 4046 helix: -0.62 (0.13), residues: 1341 sheet: -1.80 (0.20), residues: 579 loop : -2.65 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 23 HIS 0.008 0.001 HIS D 777 PHE 0.021 0.002 PHE C1323 TYR 0.030 0.002 TYR D 795 ARG 0.013 0.001 ARG G 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 491 time to evaluate : 4.015 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: A 226 GLU cc_start: 0.8746 (tt0) cc_final: 0.8114 (tt0) REVERT: C 26 TYR cc_start: 0.8505 (t80) cc_final: 0.7696 (t80) REVERT: C 84 GLU cc_start: 0.7757 (mp0) cc_final: 0.7404 (mp0) REVERT: C 100 LEU cc_start: 0.9163 (mt) cc_final: 0.8951 (mm) REVERT: C 105 TYR cc_start: 0.8962 (m-10) cc_final: 0.8686 (m-80) REVERT: C 133 ASN cc_start: 0.7931 (m-40) cc_final: 0.7720 (m-40) REVERT: C 151 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7040 (mtm110) REVERT: C 336 LEU cc_start: 0.8855 (pp) cc_final: 0.8602 (pp) REVERT: C 394 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7921 (mmt180) REVERT: C 434 ASP cc_start: 0.9016 (m-30) cc_final: 0.8772 (m-30) REVERT: C 443 ASP cc_start: 0.9259 (m-30) cc_final: 0.9004 (m-30) REVERT: C 461 GLU cc_start: 0.8043 (pp20) cc_final: 0.7801 (pp20) REVERT: C 488 MET cc_start: 0.8395 (mmm) cc_final: 0.8105 (mmm) REVERT: C 515 MET cc_start: 0.6964 (ttt) cc_final: 0.6617 (ttt) REVERT: C 672 GLU cc_start: 0.8411 (pm20) cc_final: 0.8049 (pm20) REVERT: C 704 MET cc_start: 0.8553 (tmm) cc_final: 0.8208 (tmm) REVERT: C 768 MET cc_start: 0.8063 (mtm) cc_final: 0.6987 (ptt) REVERT: C 878 THR cc_start: 0.7344 (p) cc_final: 0.6875 (t) REVERT: C 931 VAL cc_start: 0.9071 (t) cc_final: 0.8826 (m) REVERT: C 1020 GLU cc_start: 0.9223 (tt0) cc_final: 0.8772 (pt0) REVERT: C 1119 MET cc_start: 0.8566 (tpp) cc_final: 0.8021 (tpp) REVERT: C 1232 MET cc_start: 0.7850 (mmm) cc_final: 0.7155 (mtp) REVERT: C 1235 LEU cc_start: 0.6895 (tp) cc_final: 0.6670 (tp) REVERT: C 1276 TRP cc_start: 0.8592 (m-10) cc_final: 0.7958 (m-90) REVERT: C 1290 MET cc_start: 0.7351 (tpp) cc_final: 0.6748 (tpp) REVERT: D 159 ILE cc_start: 0.9257 (pt) cc_final: 0.8208 (pt) REVERT: D 164 GLN cc_start: 0.9136 (mt0) cc_final: 0.8896 (mt0) REVERT: D 201 LEU cc_start: 0.9108 (mt) cc_final: 0.8287 (tt) REVERT: D 227 PHE cc_start: 0.8884 (m-80) cc_final: 0.8613 (m-80) REVERT: D 248 ASP cc_start: 0.8122 (m-30) cc_final: 0.7678 (t0) REVERT: D 330 MET cc_start: 0.5836 (mmt) cc_final: 0.5529 (mtp) REVERT: D 438 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8171 (mt-10) REVERT: D 478 LEU cc_start: 0.8573 (mt) cc_final: 0.8248 (mt) REVERT: D 479 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7370 (mt-10) REVERT: D 484 MET cc_start: 0.8074 (mpp) cc_final: 0.7850 (mpp) REVERT: D 555 TYR cc_start: 0.8364 (m-10) cc_final: 0.8043 (m-10) REVERT: D 569 LEU cc_start: 0.8922 (tp) cc_final: 0.8439 (mp) REVERT: D 571 ASP cc_start: 0.8368 (t0) cc_final: 0.8140 (t0) REVERT: D 697 MET cc_start: 0.7600 (tmm) cc_final: 0.7364 (tmm) REVERT: D 743 MET cc_start: 0.7483 (ptm) cc_final: 0.7152 (ptp) REVERT: D 1040 MET cc_start: 0.6454 (ttp) cc_final: 0.6251 (ttp) REVERT: F 48 MET cc_start: 0.9081 (tmm) cc_final: 0.8867 (tmm) REVERT: F 74 ASP cc_start: 0.9057 (t0) cc_final: 0.8678 (t0) REVERT: F 83 LEU cc_start: 0.8795 (tt) cc_final: 0.8583 (mm) REVERT: F 119 LYS cc_start: 0.8361 (ptmt) cc_final: 0.7486 (pttt) REVERT: K 40 ASN cc_start: 0.9294 (t0) cc_final: 0.8992 (t0) REVERT: K 55 TYR cc_start: 0.8894 (m-80) cc_final: 0.8690 (m-80) REVERT: K 86 GLN cc_start: 0.9207 (mt0) cc_final: 0.8939 (mt0) REVERT: K 93 ASN cc_start: 0.8719 (t0) cc_final: 0.8412 (t0) REVERT: E 11 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6437 (mm-30) REVERT: E 52 ARG cc_start: 0.7126 (mtp180) cc_final: 0.6178 (tpp-160) REVERT: H 1 MET cc_start: 0.7825 (ttt) cc_final: 0.7571 (ttt) REVERT: I 1 MET cc_start: 0.7274 (ttm) cc_final: 0.6901 (ttt) REVERT: I 187 MET cc_start: 0.8115 (tpt) cc_final: 0.7094 (tpt) REVERT: I 189 MET cc_start: 0.5585 (ptp) cc_final: 0.3884 (ptp) outliers start: 4 outliers final: 2 residues processed: 494 average time/residue: 0.4898 time to fit residues: 385.4520 Evaluate side-chains 381 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 379 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 368 optimal weight: 8.9990 chunk 280 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 250 optimal weight: 0.8980 chunk 374 optimal weight: 2.9990 chunk 396 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 354 optimal weight: 30.0000 chunk 106 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN C 952 GLN ** C 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1135 GLN C1175 ASN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN H 213 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34467 Z= 0.191 Angle : 0.627 10.125 46973 Z= 0.329 Chirality : 0.043 0.255 5376 Planarity : 0.004 0.086 5798 Dihedral : 16.397 128.008 5465 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -2.10 (0.13), residues: 4046 helix: 0.03 (0.14), residues: 1349 sheet: -1.59 (0.20), residues: 588 loop : -2.36 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 807 HIS 0.004 0.001 HIS D1252 PHE 0.014 0.001 PHE C1323 TYR 0.014 0.001 TYR F 63 ARG 0.035 0.001 ARG K 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 528 time to evaluate : 3.697 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: A 205 MET cc_start: 0.7060 (ptm) cc_final: 0.6115 (ptm) REVERT: A 226 GLU cc_start: 0.8557 (tt0) cc_final: 0.8316 (tt0) REVERT: C 84 GLU cc_start: 0.7912 (mp0) cc_final: 0.7691 (mp0) REVERT: C 105 TYR cc_start: 0.8850 (m-10) cc_final: 0.8560 (m-80) REVERT: C 133 ASN cc_start: 0.7785 (m-40) cc_final: 0.7572 (m-40) REVERT: C 151 ARG cc_start: 0.8119 (mtp180) cc_final: 0.6924 (mtm110) REVERT: C 185 ASP cc_start: 0.7912 (t0) cc_final: 0.7646 (t0) REVERT: C 394 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7819 (mmt180) REVERT: C 434 ASP cc_start: 0.9092 (m-30) cc_final: 0.8737 (m-30) REVERT: C 515 MET cc_start: 0.6598 (ttt) cc_final: 0.6100 (ttt) REVERT: C 672 GLU cc_start: 0.8280 (pm20) cc_final: 0.8043 (pm20) REVERT: C 704 MET cc_start: 0.8130 (tmm) cc_final: 0.7163 (tmm) REVERT: C 768 MET cc_start: 0.8195 (mtm) cc_final: 0.7176 (ptt) REVERT: C 878 THR cc_start: 0.7191 (p) cc_final: 0.6796 (t) REVERT: C 881 ASP cc_start: 0.8106 (t70) cc_final: 0.7762 (t70) REVERT: C 931 VAL cc_start: 0.9050 (t) cc_final: 0.8652 (m) REVERT: C 1020 GLU cc_start: 0.9404 (tt0) cc_final: 0.8996 (pt0) REVERT: C 1119 MET cc_start: 0.8441 (tpp) cc_final: 0.7930 (tpp) REVERT: C 1176 LEU cc_start: 0.9107 (mm) cc_final: 0.8838 (mm) REVERT: C 1178 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8242 (mmmt) REVERT: C 1195 ILE cc_start: 0.7707 (mm) cc_final: 0.7501 (mm) REVERT: C 1230 MET cc_start: 0.5404 (ttp) cc_final: 0.4911 (ptm) REVERT: C 1232 MET cc_start: 0.7944 (mmm) cc_final: 0.7144 (mtp) REVERT: C 1272 GLU cc_start: 0.7030 (pt0) cc_final: 0.6600 (pt0) REVERT: C 1276 TRP cc_start: 0.8619 (m-10) cc_final: 0.7856 (m-90) REVERT: C 1291 LEU cc_start: 0.8618 (pt) cc_final: 0.8358 (tt) REVERT: D 136 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8760 (tp30) REVERT: D 160 LEU cc_start: 0.9004 (mm) cc_final: 0.8725 (mm) REVERT: D 164 GLN cc_start: 0.9099 (mt0) cc_final: 0.8804 (mt0) REVERT: D 227 PHE cc_start: 0.8790 (m-80) cc_final: 0.8442 (m-10) REVERT: D 237 MET cc_start: 0.7702 (mtt) cc_final: 0.7435 (mtt) REVERT: D 248 ASP cc_start: 0.8265 (m-30) cc_final: 0.7826 (t0) REVERT: D 330 MET cc_start: 0.5877 (mmt) cc_final: 0.5619 (mtp) REVERT: D 345 LYS cc_start: 0.7782 (ptpp) cc_final: 0.7525 (ptmt) REVERT: D 398 LYS cc_start: 0.8376 (mttt) cc_final: 0.7906 (ptpt) REVERT: D 438 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 478 LEU cc_start: 0.8526 (mt) cc_final: 0.8178 (mt) REVERT: D 479 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6953 (mt-10) REVERT: D 484 MET cc_start: 0.8066 (mpp) cc_final: 0.7693 (mpp) REVERT: D 555 TYR cc_start: 0.8171 (m-10) cc_final: 0.7846 (m-10) REVERT: D 569 LEU cc_start: 0.8886 (tp) cc_final: 0.8458 (mp) REVERT: D 571 ASP cc_start: 0.8470 (t0) cc_final: 0.8242 (t0) REVERT: D 644 MET cc_start: 0.6242 (mpp) cc_final: 0.5064 (mpp) REVERT: D 697 MET cc_start: 0.7385 (tmm) cc_final: 0.7157 (tmm) REVERT: D 724 MET cc_start: 0.8048 (mtp) cc_final: 0.7727 (mtt) REVERT: D 743 MET cc_start: 0.7365 (ptm) cc_final: 0.6956 (ptm) REVERT: D 1040 MET cc_start: 0.7045 (ttp) cc_final: 0.6752 (ttp) REVERT: D 1219 ASP cc_start: 0.8924 (t0) cc_final: 0.8632 (t0) REVERT: D 1260 MET cc_start: 0.8606 (mmm) cc_final: 0.8168 (mmm) REVERT: D 1345 ARG cc_start: 0.7107 (mmt90) cc_final: 0.6815 (mmt90) REVERT: D 1349 GLU cc_start: 0.7735 (pm20) cc_final: 0.7509 (pm20) REVERT: D 1370 MET cc_start: 0.8217 (tpt) cc_final: 0.7976 (tpp) REVERT: F 48 MET cc_start: 0.9050 (tmm) cc_final: 0.8809 (tmm) REVERT: F 74 ASP cc_start: 0.9062 (t0) cc_final: 0.8713 (t0) REVERT: F 113 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8103 (mm-30) REVERT: F 119 LYS cc_start: 0.8250 (ptmt) cc_final: 0.7833 (pttt) REVERT: F 134 ASP cc_start: 0.8094 (t0) cc_final: 0.7834 (t0) REVERT: K 40 ASN cc_start: 0.9275 (t0) cc_final: 0.9062 (t0) REVERT: K 86 GLN cc_start: 0.9174 (mt0) cc_final: 0.8971 (mt0) REVERT: K 93 ASN cc_start: 0.8707 (t0) cc_final: 0.8437 (t0) REVERT: E 19 LEU cc_start: 0.6920 (tt) cc_final: 0.6573 (mm) REVERT: E 52 ARG cc_start: 0.6970 (mtp180) cc_final: 0.6056 (tpp-160) REVERT: E 60 ASN cc_start: 0.7747 (p0) cc_final: 0.7439 (p0) REVERT: E 63 ILE cc_start: 0.9124 (mm) cc_final: 0.8885 (mm) REVERT: E 67 ARG cc_start: 0.9083 (ttm110) cc_final: 0.8563 (mtm110) REVERT: G 1 MET cc_start: 0.9182 (ptm) cc_final: 0.8787 (ptm) REVERT: G 22 MET cc_start: 0.7998 (pmm) cc_final: 0.7671 (pmm) REVERT: G 126 LEU cc_start: 0.9760 (tt) cc_final: 0.9529 (pp) REVERT: H 1 MET cc_start: 0.7797 (ttt) cc_final: 0.7512 (ttt) REVERT: H 184 MET cc_start: 0.6665 (mmm) cc_final: 0.6162 (mmm) REVERT: H 187 MET cc_start: 0.2307 (mtm) cc_final: 0.1504 (ttm) REVERT: I 1 MET cc_start: 0.7097 (ttm) cc_final: 0.6641 (ttt) REVERT: I 187 MET cc_start: 0.8251 (tpt) cc_final: 0.6880 (tpt) REVERT: I 189 MET cc_start: 0.5466 (ptp) cc_final: 0.3686 (mtp) outliers start: 2 outliers final: 1 residues processed: 529 average time/residue: 0.4915 time to fit residues: 413.6544 Evaluate side-chains 395 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 330 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 295 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 338 optimal weight: 0.0970 chunk 273 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 355 optimal weight: 30.0000 chunk 100 optimal weight: 0.6980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 HIS C 628 HIS ** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 875 ASN H 213 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34467 Z= 0.179 Angle : 0.608 10.717 46973 Z= 0.317 Chirality : 0.043 0.236 5376 Planarity : 0.004 0.061 5798 Dihedral : 16.274 127.122 5465 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.35 % Favored : 93.62 % Rotamer: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -1.79 (0.13), residues: 4046 helix: 0.35 (0.14), residues: 1356 sheet: -1.40 (0.20), residues: 590 loop : -2.23 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 997 HIS 0.004 0.001 HIS C 554 PHE 0.023 0.001 PHE F 106 TYR 0.020 0.001 TYR C1229 ARG 0.016 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 513 time to evaluate : 3.870 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: A 226 GLU cc_start: 0.8662 (tt0) cc_final: 0.8137 (tm-30) REVERT: B 85 LEU cc_start: 0.9574 (mt) cc_final: 0.9349 (pp) REVERT: C 84 GLU cc_start: 0.7870 (mp0) cc_final: 0.7585 (mp0) REVERT: C 105 TYR cc_start: 0.8741 (m-10) cc_final: 0.8449 (m-80) REVERT: C 151 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7103 (mtm110) REVERT: C 185 ASP cc_start: 0.7953 (t0) cc_final: 0.7414 (t0) REVERT: C 394 ARG cc_start: 0.8160 (mtt90) cc_final: 0.7790 (mmt180) REVERT: C 515 MET cc_start: 0.6608 (ttt) cc_final: 0.6137 (ttt) REVERT: C 672 GLU cc_start: 0.8097 (pm20) cc_final: 0.7657 (pt0) REVERT: C 704 MET cc_start: 0.8242 (tmm) cc_final: 0.7070 (tmm) REVERT: C 768 MET cc_start: 0.8098 (mtm) cc_final: 0.7104 (ptt) REVERT: C 813 GLU cc_start: 0.7530 (tp30) cc_final: 0.6792 (tt0) REVERT: C 878 THR cc_start: 0.7133 (p) cc_final: 0.6707 (t) REVERT: C 881 ASP cc_start: 0.8131 (t70) cc_final: 0.7808 (t70) REVERT: C 931 VAL cc_start: 0.9081 (t) cc_final: 0.8674 (m) REVERT: C 1020 GLU cc_start: 0.9385 (tt0) cc_final: 0.8945 (pt0) REVERT: C 1066 MET cc_start: 0.8034 (ttm) cc_final: 0.7394 (ttm) REVERT: C 1119 MET cc_start: 0.8479 (tpp) cc_final: 0.8192 (tpp) REVERT: C 1176 LEU cc_start: 0.9112 (mm) cc_final: 0.8902 (mm) REVERT: C 1178 LYS cc_start: 0.8751 (mtpp) cc_final: 0.8205 (mmmt) REVERT: C 1195 ILE cc_start: 0.7769 (mm) cc_final: 0.7517 (mm) REVERT: C 1230 MET cc_start: 0.5468 (ttp) cc_final: 0.4813 (ptm) REVERT: C 1232 MET cc_start: 0.7954 (mmm) cc_final: 0.6915 (mtp) REVERT: C 1243 MET cc_start: 0.7305 (tmm) cc_final: 0.6949 (tmm) REVERT: C 1272 GLU cc_start: 0.6988 (pt0) cc_final: 0.6191 (pt0) REVERT: C 1276 TRP cc_start: 0.8494 (m-10) cc_final: 0.7350 (m-90) REVERT: C 1290 MET cc_start: 0.7279 (tpp) cc_final: 0.6700 (tpp) REVERT: C 1291 LEU cc_start: 0.8591 (pt) cc_final: 0.8253 (tt) REVERT: D 134 ASP cc_start: 0.8630 (t70) cc_final: 0.8251 (t0) REVERT: D 136 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8651 (tp30) REVERT: D 160 LEU cc_start: 0.8803 (mm) cc_final: 0.8511 (mm) REVERT: D 164 GLN cc_start: 0.9110 (mt0) cc_final: 0.8857 (mt0) REVERT: D 201 LEU cc_start: 0.9043 (mt) cc_final: 0.8696 (mt) REVERT: D 227 PHE cc_start: 0.8630 (m-80) cc_final: 0.8231 (m-10) REVERT: D 237 MET cc_start: 0.7692 (mtt) cc_final: 0.7421 (mtt) REVERT: D 248 ASP cc_start: 0.8292 (m-30) cc_final: 0.7871 (t0) REVERT: D 330 MET cc_start: 0.6177 (mmt) cc_final: 0.5560 (mtp) REVERT: D 345 LYS cc_start: 0.7340 (ptpp) cc_final: 0.7068 (ptmt) REVERT: D 438 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8196 (mt-10) REVERT: D 478 LEU cc_start: 0.8525 (mt) cc_final: 0.8185 (mt) REVERT: D 479 GLU cc_start: 0.7706 (mt-10) cc_final: 0.6794 (mt-10) REVERT: D 484 MET cc_start: 0.7996 (mpp) cc_final: 0.7551 (mpp) REVERT: D 485 MET cc_start: 0.7896 (ttp) cc_final: 0.6591 (ptp) REVERT: D 569 LEU cc_start: 0.8848 (tp) cc_final: 0.8345 (mp) REVERT: D 571 ASP cc_start: 0.8396 (t0) cc_final: 0.8135 (t0) REVERT: D 625 MET cc_start: 0.7922 (tmm) cc_final: 0.7261 (tmm) REVERT: D 644 MET cc_start: 0.6116 (mpp) cc_final: 0.5156 (mpp) REVERT: D 714 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7960 (mp0) REVERT: D 724 MET cc_start: 0.8086 (mtp) cc_final: 0.7714 (mtt) REVERT: D 743 MET cc_start: 0.7389 (ptm) cc_final: 0.6950 (ptm) REVERT: D 1219 ASP cc_start: 0.8868 (t0) cc_final: 0.8555 (t0) REVERT: D 1345 ARG cc_start: 0.7055 (mmt90) cc_final: 0.6746 (mmt90) REVERT: D 1370 MET cc_start: 0.8182 (tpt) cc_final: 0.7972 (tpp) REVERT: F 48 MET cc_start: 0.8992 (tmm) cc_final: 0.8717 (tmm) REVERT: F 74 ASP cc_start: 0.9101 (t0) cc_final: 0.8729 (t0) REVERT: F 119 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7693 (pttt) REVERT: F 134 ASP cc_start: 0.8066 (t0) cc_final: 0.7789 (t0) REVERT: K 40 ASN cc_start: 0.9301 (t0) cc_final: 0.8978 (t0) REVERT: K 93 ASN cc_start: 0.8696 (t0) cc_final: 0.8465 (t0) REVERT: E 19 LEU cc_start: 0.6868 (tt) cc_final: 0.6566 (mm) REVERT: E 42 GLU cc_start: 0.6760 (mp0) cc_final: 0.6335 (mp0) REVERT: E 44 ASP cc_start: 0.7114 (m-30) cc_final: 0.6815 (p0) REVERT: E 59 ILE cc_start: 0.7782 (tt) cc_final: 0.7269 (tt) REVERT: E 60 ASN cc_start: 0.7803 (p0) cc_final: 0.7459 (p0) REVERT: E 63 ILE cc_start: 0.9096 (mm) cc_final: 0.8880 (mm) REVERT: E 67 ARG cc_start: 0.9014 (ttm110) cc_final: 0.8515 (mtm110) REVERT: G 1 MET cc_start: 0.9145 (ptm) cc_final: 0.8745 (ptm) REVERT: G 22 MET cc_start: 0.7991 (pmm) cc_final: 0.7661 (pmm) REVERT: G 27 GLN cc_start: 0.8779 (pp30) cc_final: 0.8462 (pp30) REVERT: G 131 ARG cc_start: 0.9379 (ptt-90) cc_final: 0.9074 (ptp90) REVERT: H 1 MET cc_start: 0.7768 (ttt) cc_final: 0.7493 (ttt) REVERT: H 184 MET cc_start: 0.6171 (mmm) cc_final: 0.5460 (mmm) REVERT: H 187 MET cc_start: 0.3131 (mtm) cc_final: 0.1775 (ttt) REVERT: I 1 MET cc_start: 0.6911 (ttm) cc_final: 0.6651 (ttt) REVERT: I 30 MET cc_start: 0.3393 (pmm) cc_final: 0.2551 (ttp) REVERT: I 165 TYR cc_start: 0.8985 (t80) cc_final: 0.8659 (t80) REVERT: I 187 MET cc_start: 0.8207 (tpt) cc_final: 0.6860 (tpt) REVERT: I 189 MET cc_start: 0.5372 (ptp) cc_final: 0.3643 (mtp) outliers start: 2 outliers final: 0 residues processed: 514 average time/residue: 0.4840 time to fit residues: 401.3886 Evaluate side-chains 392 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 133 optimal weight: 9.9990 chunk 356 optimal weight: 50.0000 chunk 78 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 396 optimal weight: 40.0000 chunk 329 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34467 Z= 0.236 Angle : 0.630 8.895 46973 Z= 0.330 Chirality : 0.044 0.317 5376 Planarity : 0.004 0.055 5798 Dihedral : 16.232 126.567 5465 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -1.71 (0.13), residues: 4046 helix: 0.42 (0.14), residues: 1343 sheet: -1.43 (0.19), residues: 650 loop : -2.15 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 997 HIS 0.005 0.001 HIS D 777 PHE 0.018 0.001 PHE D1037 TYR 0.027 0.001 TYR C1229 ARG 0.014 0.001 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 4.066 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: A 25 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8689 (mmmt) REVERT: A 66 HIS cc_start: 0.8762 (OUTLIER) cc_final: 0.8517 (p90) REVERT: A 226 GLU cc_start: 0.8648 (tt0) cc_final: 0.8121 (tm-30) REVERT: B 85 LEU cc_start: 0.9551 (mt) cc_final: 0.9318 (pp) REVERT: B 205 MET cc_start: 0.8539 (tmm) cc_final: 0.8325 (tmm) REVERT: C 84 GLU cc_start: 0.7878 (mp0) cc_final: 0.7597 (mp0) REVERT: C 133 ASN cc_start: 0.7856 (m-40) cc_final: 0.7636 (m-40) REVERT: C 151 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7110 (mtm110) REVERT: C 185 ASP cc_start: 0.7927 (t0) cc_final: 0.7203 (t0) REVERT: C 394 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7801 (mmt180) REVERT: C 478 ARG cc_start: 0.8722 (mmp80) cc_final: 0.8316 (mmp80) REVERT: C 672 GLU cc_start: 0.8031 (pm20) cc_final: 0.7825 (pt0) REVERT: C 704 MET cc_start: 0.8383 (tmm) cc_final: 0.6892 (tmm) REVERT: C 768 MET cc_start: 0.8258 (mtm) cc_final: 0.7115 (ptt) REVERT: C 813 GLU cc_start: 0.7796 (tp30) cc_final: 0.6887 (tt0) REVERT: C 878 THR cc_start: 0.7428 (p) cc_final: 0.6958 (t) REVERT: C 881 ASP cc_start: 0.8268 (t70) cc_final: 0.7792 (t0) REVERT: C 931 VAL cc_start: 0.9116 (t) cc_final: 0.8745 (m) REVERT: C 1119 MET cc_start: 0.8502 (tpp) cc_final: 0.8196 (tpp) REVERT: C 1178 LYS cc_start: 0.8881 (mtpp) cc_final: 0.8256 (mmmt) REVERT: C 1195 ILE cc_start: 0.7787 (mm) cc_final: 0.7536 (mm) REVERT: C 1232 MET cc_start: 0.7841 (mmm) cc_final: 0.6778 (mtp) REVERT: C 1243 MET cc_start: 0.7262 (tmm) cc_final: 0.6794 (tmm) REVERT: C 1272 GLU cc_start: 0.6940 (pt0) cc_final: 0.6105 (pt0) REVERT: C 1276 TRP cc_start: 0.8585 (m-10) cc_final: 0.7669 (m-90) REVERT: C 1291 LEU cc_start: 0.8640 (pt) cc_final: 0.8353 (tt) REVERT: D 134 ASP cc_start: 0.8675 (t70) cc_final: 0.8326 (t0) REVERT: D 160 LEU cc_start: 0.8800 (mm) cc_final: 0.8501 (mm) REVERT: D 164 GLN cc_start: 0.9085 (mt0) cc_final: 0.8818 (mt0) REVERT: D 201 LEU cc_start: 0.9139 (mt) cc_final: 0.8790 (mt) REVERT: D 227 PHE cc_start: 0.8662 (m-80) cc_final: 0.8225 (m-10) REVERT: D 248 ASP cc_start: 0.8176 (m-30) cc_final: 0.7831 (t0) REVERT: D 330 MET cc_start: 0.6159 (mmt) cc_final: 0.5623 (mtp) REVERT: D 345 LYS cc_start: 0.7985 (ptpp) cc_final: 0.7707 (ptmt) REVERT: D 438 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7993 (mt-10) REVERT: D 478 LEU cc_start: 0.8553 (mt) cc_final: 0.8199 (mt) REVERT: D 479 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7021 (mt-10) REVERT: D 484 MET cc_start: 0.8023 (mpp) cc_final: 0.7711 (mpp) REVERT: D 485 MET cc_start: 0.7893 (ttp) cc_final: 0.6468 (ptp) REVERT: D 571 ASP cc_start: 0.8372 (t0) cc_final: 0.8124 (t0) REVERT: D 644 MET cc_start: 0.6326 (mpp) cc_final: 0.5288 (mpp) REVERT: D 714 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7899 (mp0) REVERT: D 724 MET cc_start: 0.7927 (mtp) cc_final: 0.7505 (mtt) REVERT: D 743 MET cc_start: 0.7353 (ptm) cc_final: 0.6910 (ptm) REVERT: D 925 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8366 (tm-30) REVERT: D 1219 ASP cc_start: 0.9002 (t0) cc_final: 0.8619 (t0) REVERT: D 1345 ARG cc_start: 0.7055 (mmt90) cc_final: 0.6669 (mmt90) REVERT: D 1370 MET cc_start: 0.8142 (tpt) cc_final: 0.7905 (tpp) REVERT: F 48 MET cc_start: 0.8901 (tmm) cc_final: 0.8619 (tmm) REVERT: F 74 ASP cc_start: 0.9136 (t0) cc_final: 0.8733 (t0) REVERT: F 119 LYS cc_start: 0.8223 (ptmt) cc_final: 0.7732 (pttt) REVERT: K 40 ASN cc_start: 0.9367 (t0) cc_final: 0.9065 (t0) REVERT: K 93 ASN cc_start: 0.8671 (t0) cc_final: 0.8431 (t0) REVERT: E 42 GLU cc_start: 0.6841 (mp0) cc_final: 0.6388 (mp0) REVERT: E 44 ASP cc_start: 0.7366 (m-30) cc_final: 0.7052 (p0) REVERT: E 49 ILE cc_start: 0.8551 (mt) cc_final: 0.8345 (mt) REVERT: E 67 ARG cc_start: 0.8984 (ttm110) cc_final: 0.8576 (mtm110) REVERT: G 1 MET cc_start: 0.9062 (ptm) cc_final: 0.8533 (ptm) REVERT: G 22 MET cc_start: 0.7948 (pmm) cc_final: 0.7683 (pmm) REVERT: G 27 GLN cc_start: 0.8733 (pp30) cc_final: 0.8420 (pp30) REVERT: H 1 MET cc_start: 0.7692 (ttt) cc_final: 0.7454 (ttt) REVERT: H 184 MET cc_start: 0.5931 (mmm) cc_final: 0.5342 (mmm) REVERT: H 187 MET cc_start: 0.3164 (mtm) cc_final: 0.2116 (ttm) REVERT: I 1 MET cc_start: 0.6977 (ttm) cc_final: 0.6704 (ttt) REVERT: I 30 MET cc_start: 0.3387 (pmm) cc_final: 0.2554 (ttp) REVERT: I 187 MET cc_start: 0.8105 (tpt) cc_final: 0.6939 (tpt) REVERT: I 189 MET cc_start: 0.5341 (ptp) cc_final: 0.3575 (mtp) outliers start: 1 outliers final: 0 residues processed: 482 average time/residue: 0.4899 time to fit residues: 378.4431 Evaluate side-chains 377 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 382 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 chunk 289 optimal weight: 7.9990 chunk 224 optimal weight: 0.6980 chunk 333 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 395 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS C 69 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN D 489 ASN ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34467 Z= 0.207 Angle : 0.616 9.681 46973 Z= 0.322 Chirality : 0.043 0.209 5376 Planarity : 0.004 0.052 5798 Dihedral : 16.188 125.714 5465 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -1.57 (0.13), residues: 4046 helix: 0.49 (0.14), residues: 1344 sheet: -1.29 (0.20), residues: 639 loop : -2.06 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 807 HIS 0.015 0.001 HIS A 66 PHE 0.020 0.001 PHE F 106 TYR 0.024 0.001 TYR C1229 ARG 0.007 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 483 time to evaluate : 3.844 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: A 25 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8795 (mmmt) REVERT: A 142 MET cc_start: 0.6774 (pmm) cc_final: 0.6019 (pmm) REVERT: A 226 GLU cc_start: 0.8645 (tt0) cc_final: 0.8177 (tm-30) REVERT: B 85 LEU cc_start: 0.9567 (mt) cc_final: 0.9354 (pp) REVERT: B 205 MET cc_start: 0.8525 (tmm) cc_final: 0.8128 (tmm) REVERT: C 84 GLU cc_start: 0.7918 (mp0) cc_final: 0.7640 (mp0) REVERT: C 133 ASN cc_start: 0.7832 (m-40) cc_final: 0.7581 (m-40) REVERT: C 151 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7097 (mtm110) REVERT: C 185 ASP cc_start: 0.7996 (t0) cc_final: 0.7223 (t0) REVERT: C 429 MET cc_start: 0.9043 (mmm) cc_final: 0.8375 (mmm) REVERT: C 611 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8304 (pm20) REVERT: C 704 MET cc_start: 0.8281 (tmm) cc_final: 0.6982 (tmm) REVERT: C 768 MET cc_start: 0.8290 (mtm) cc_final: 0.7103 (ptt) REVERT: C 813 GLU cc_start: 0.7727 (tp30) cc_final: 0.7009 (tt0) REVERT: C 878 THR cc_start: 0.7374 (p) cc_final: 0.6912 (t) REVERT: C 881 ASP cc_start: 0.8447 (t70) cc_final: 0.7964 (t0) REVERT: C 931 VAL cc_start: 0.9139 (t) cc_final: 0.8757 (m) REVERT: C 1119 MET cc_start: 0.8504 (tpp) cc_final: 0.8201 (tpp) REVERT: C 1178 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8287 (mmmt) REVERT: C 1195 ILE cc_start: 0.7882 (mm) cc_final: 0.7637 (mm) REVERT: C 1230 MET cc_start: 0.5645 (ttp) cc_final: 0.5097 (ptm) REVERT: C 1232 MET cc_start: 0.7752 (mmm) cc_final: 0.6712 (mtp) REVERT: C 1272 GLU cc_start: 0.6822 (pt0) cc_final: 0.5928 (pt0) REVERT: C 1276 TRP cc_start: 0.8524 (m-10) cc_final: 0.7389 (m-90) REVERT: C 1290 MET cc_start: 0.7762 (tpp) cc_final: 0.7169 (tpp) REVERT: D 134 ASP cc_start: 0.8672 (t70) cc_final: 0.8330 (t0) REVERT: D 160 LEU cc_start: 0.8750 (mm) cc_final: 0.8523 (mm) REVERT: D 201 LEU cc_start: 0.9154 (mt) cc_final: 0.8821 (mt) REVERT: D 248 ASP cc_start: 0.8195 (m-30) cc_final: 0.7865 (t0) REVERT: D 282 LEU cc_start: 0.9255 (mt) cc_final: 0.9032 (tt) REVERT: D 330 MET cc_start: 0.6206 (mmt) cc_final: 0.5631 (mtp) REVERT: D 375 GLU cc_start: 0.8235 (mp0) cc_final: 0.8015 (mp0) REVERT: D 438 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8060 (mt-10) REVERT: D 478 LEU cc_start: 0.8523 (mt) cc_final: 0.8172 (mt) REVERT: D 479 GLU cc_start: 0.7802 (mt-10) cc_final: 0.6993 (mt-10) REVERT: D 484 MET cc_start: 0.8097 (mpp) cc_final: 0.7784 (mpp) REVERT: D 485 MET cc_start: 0.7828 (ttp) cc_final: 0.6446 (ptp) REVERT: D 569 LEU cc_start: 0.9008 (tp) cc_final: 0.8671 (mp) REVERT: D 571 ASP cc_start: 0.8367 (t0) cc_final: 0.8128 (t0) REVERT: D 625 MET cc_start: 0.7909 (tmm) cc_final: 0.7432 (tmm) REVERT: D 644 MET cc_start: 0.6286 (mpp) cc_final: 0.5240 (mpp) REVERT: D 714 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7846 (mp0) REVERT: D 743 MET cc_start: 0.7335 (ptm) cc_final: 0.6924 (ptm) REVERT: D 925 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8289 (tm-30) REVERT: D 1219 ASP cc_start: 0.9005 (t0) cc_final: 0.8599 (t0) REVERT: D 1345 ARG cc_start: 0.7111 (mmt90) cc_final: 0.6763 (mmt90) REVERT: D 1370 MET cc_start: 0.8246 (tpt) cc_final: 0.8009 (tpp) REVERT: F 48 MET cc_start: 0.8892 (tmm) cc_final: 0.8581 (tmm) REVERT: F 74 ASP cc_start: 0.9059 (t0) cc_final: 0.8672 (t0) REVERT: F 91 TYR cc_start: 0.8282 (m-10) cc_final: 0.7980 (m-80) REVERT: F 119 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7712 (pttt) REVERT: K 40 ASN cc_start: 0.9366 (t0) cc_final: 0.9100 (t0) REVERT: K 93 ASN cc_start: 0.8725 (t0) cc_final: 0.8408 (t0) REVERT: E 35 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7866 (tppt) REVERT: E 52 ARG cc_start: 0.7036 (ttm170) cc_final: 0.6781 (tpp-160) REVERT: E 60 ASN cc_start: 0.7656 (p0) cc_final: 0.7415 (p0) REVERT: E 67 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8514 (mtm110) REVERT: G 1 MET cc_start: 0.9220 (ptm) cc_final: 0.8558 (ttt) REVERT: G 22 MET cc_start: 0.7781 (pmm) cc_final: 0.7531 (pmm) REVERT: G 27 GLN cc_start: 0.8736 (pp30) cc_final: 0.8416 (pp30) REVERT: H 87 ARG cc_start: 0.9100 (ttm-80) cc_final: 0.8826 (ttt180) REVERT: H 184 MET cc_start: 0.5778 (mmm) cc_final: 0.5202 (mmm) REVERT: H 187 MET cc_start: 0.3219 (mtm) cc_final: 0.2035 (ttm) REVERT: I 1 MET cc_start: 0.7243 (ttm) cc_final: 0.6906 (ttt) REVERT: I 187 MET cc_start: 0.7983 (tpt) cc_final: 0.6889 (tpt) REVERT: I 189 MET cc_start: 0.5412 (ptp) cc_final: 0.3800 (mtp) outliers start: 1 outliers final: 0 residues processed: 484 average time/residue: 0.4748 time to fit residues: 373.3217 Evaluate side-chains 376 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 244 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 269 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 310 optimal weight: 7.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 227 GLN C 69 GLN ** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 HIS I 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 34467 Z= 0.334 Angle : 0.689 13.228 46973 Z= 0.360 Chirality : 0.045 0.176 5376 Planarity : 0.005 0.094 5798 Dihedral : 16.238 124.867 5465 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.06 % Allowed : 1.19 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -1.73 (0.13), residues: 4046 helix: 0.31 (0.14), residues: 1347 sheet: -1.33 (0.20), residues: 630 loop : -2.15 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 807 HIS 0.008 0.001 HIS C 673 PHE 0.016 0.002 PHE C1265 TYR 0.027 0.002 TYR C1229 ARG 0.014 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 460 time to evaluate : 3.953 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: A 205 MET cc_start: 0.6766 (pmm) cc_final: 0.6510 (pmm) REVERT: A 226 GLU cc_start: 0.8535 (tt0) cc_final: 0.8162 (tm-30) REVERT: B 205 MET cc_start: 0.8515 (tmm) cc_final: 0.8067 (tmm) REVERT: C 84 GLU cc_start: 0.7939 (mp0) cc_final: 0.7199 (mt-10) REVERT: C 133 ASN cc_start: 0.7827 (m-40) cc_final: 0.6957 (t0) REVERT: C 185 ASP cc_start: 0.8056 (t0) cc_final: 0.7154 (t0) REVERT: C 429 MET cc_start: 0.9073 (mmm) cc_final: 0.8398 (mmm) REVERT: C 459 MET cc_start: 0.7964 (mtp) cc_final: 0.7728 (mtm) REVERT: C 478 ARG cc_start: 0.8774 (mmp80) cc_final: 0.8344 (mmp80) REVERT: C 515 MET cc_start: 0.6924 (ttt) cc_final: 0.6593 (ttt) REVERT: C 768 MET cc_start: 0.8178 (mtm) cc_final: 0.6975 (ptt) REVERT: C 813 GLU cc_start: 0.7982 (tp30) cc_final: 0.6933 (tt0) REVERT: C 878 THR cc_start: 0.7590 (p) cc_final: 0.7138 (t) REVERT: C 931 VAL cc_start: 0.9178 (t) cc_final: 0.8793 (m) REVERT: C 1119 MET cc_start: 0.8523 (tpp) cc_final: 0.8193 (tpp) REVERT: C 1178 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8333 (mmmt) REVERT: C 1232 MET cc_start: 0.7909 (mmm) cc_final: 0.6936 (mtp) REVERT: C 1272 GLU cc_start: 0.6805 (pt0) cc_final: 0.5754 (pt0) REVERT: C 1276 TRP cc_start: 0.8641 (m-10) cc_final: 0.7739 (m-90) REVERT: C 1290 MET cc_start: 0.7985 (tpp) cc_final: 0.7143 (tpp) REVERT: D 49 PHE cc_start: 0.7912 (m-80) cc_final: 0.7541 (m-80) REVERT: D 134 ASP cc_start: 0.8655 (t70) cc_final: 0.8311 (t0) REVERT: D 160 LEU cc_start: 0.8847 (mm) cc_final: 0.8382 (mm) REVERT: D 164 GLN cc_start: 0.9023 (mt0) cc_final: 0.8651 (mt0) REVERT: D 248 ASP cc_start: 0.8086 (m-30) cc_final: 0.7730 (t0) REVERT: D 282 LEU cc_start: 0.9244 (mt) cc_final: 0.8979 (tt) REVERT: D 330 MET cc_start: 0.6225 (mmt) cc_final: 0.5755 (mtp) REVERT: D 398 LYS cc_start: 0.8406 (pttt) cc_final: 0.8102 (pttm) REVERT: D 438 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7954 (mt-10) REVERT: D 478 LEU cc_start: 0.8600 (mt) cc_final: 0.8289 (mt) REVERT: D 479 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7251 (mt-10) REVERT: D 484 MET cc_start: 0.8098 (mpp) cc_final: 0.7700 (mpp) REVERT: D 485 MET cc_start: 0.7943 (ttp) cc_final: 0.6237 (ptp) REVERT: D 492 SER cc_start: 0.8119 (t) cc_final: 0.7735 (p) REVERT: D 569 LEU cc_start: 0.8975 (tp) cc_final: 0.8530 (mp) REVERT: D 644 MET cc_start: 0.6420 (mpp) cc_final: 0.5952 (mpp) REVERT: D 714 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7859 (mp0) REVERT: D 724 MET cc_start: 0.7693 (mtt) cc_final: 0.7429 (mtt) REVERT: D 743 MET cc_start: 0.7283 (ptm) cc_final: 0.6857 (ptm) REVERT: D 1219 ASP cc_start: 0.9054 (t0) cc_final: 0.8675 (t0) REVERT: D 1345 ARG cc_start: 0.7022 (mmt90) cc_final: 0.6604 (mmt90) REVERT: D 1370 MET cc_start: 0.8132 (tpt) cc_final: 0.7846 (tpp) REVERT: F 74 ASP cc_start: 0.9117 (t0) cc_final: 0.8615 (t0) REVERT: F 91 TYR cc_start: 0.8485 (m-10) cc_final: 0.8107 (m-80) REVERT: F 113 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7937 (mm-30) REVERT: F 116 GLU cc_start: 0.8625 (pp20) cc_final: 0.8322 (pp20) REVERT: F 119 LYS cc_start: 0.8295 (ptmt) cc_final: 0.7845 (pttt) REVERT: F 134 ASP cc_start: 0.8260 (t70) cc_final: 0.7943 (t0) REVERT: K 40 ASN cc_start: 0.9386 (t0) cc_final: 0.9127 (t0) REVERT: K 93 ASN cc_start: 0.8786 (t0) cc_final: 0.8400 (t0) REVERT: E 29 GLN cc_start: 0.9485 (tt0) cc_final: 0.8915 (tm-30) REVERT: E 42 GLU cc_start: 0.6782 (mp0) cc_final: 0.6540 (mp0) REVERT: E 54 ILE cc_start: 0.8288 (mt) cc_final: 0.7972 (mt) REVERT: E 59 ILE cc_start: 0.7640 (tt) cc_final: 0.7377 (pt) REVERT: E 60 ASN cc_start: 0.7652 (p0) cc_final: 0.7392 (p0) REVERT: E 67 ARG cc_start: 0.8976 (ttm110) cc_final: 0.8577 (mtm110) REVERT: G 1 MET cc_start: 0.9084 (ptm) cc_final: 0.8486 (ptm) REVERT: G 22 MET cc_start: 0.7885 (pmm) cc_final: 0.7669 (pmm) REVERT: G 27 GLN cc_start: 0.8704 (pp30) cc_final: 0.8319 (pp30) REVERT: G 131 ARG cc_start: 0.9409 (ptt-90) cc_final: 0.9086 (ptp90) REVERT: H 1 MET cc_start: 0.8227 (ttt) cc_final: 0.7905 (ttt) REVERT: H 184 MET cc_start: 0.5987 (mmm) cc_final: 0.5412 (mmm) REVERT: H 187 MET cc_start: 0.3255 (mtm) cc_final: 0.2084 (ttm) REVERT: I 1 MET cc_start: 0.7173 (ttm) cc_final: 0.6820 (ttt) REVERT: I 187 MET cc_start: 0.7991 (tpt) cc_final: 0.6892 (tpt) REVERT: I 189 MET cc_start: 0.5448 (ptp) cc_final: 0.3804 (mtp) outliers start: 2 outliers final: 0 residues processed: 462 average time/residue: 0.4790 time to fit residues: 360.9758 Evaluate side-chains 354 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 359 optimal weight: 7.9990 chunk 378 optimal weight: 6.9990 chunk 345 optimal weight: 50.0000 chunk 368 optimal weight: 30.0000 chunk 221 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 289 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 chunk 332 optimal weight: 3.9990 chunk 348 optimal weight: 30.0000 chunk 366 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 649 GLN ** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN G 13 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34467 Z= 0.286 Angle : 0.669 11.765 46973 Z= 0.350 Chirality : 0.044 0.227 5376 Planarity : 0.005 0.104 5798 Dihedral : 16.247 124.045 5465 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.32 % Favored : 92.66 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -1.65 (0.13), residues: 4046 helix: 0.33 (0.14), residues: 1345 sheet: -1.12 (0.21), residues: 578 loop : -2.10 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 807 HIS 0.007 0.001 HIS C1237 PHE 0.018 0.001 PHE D 629 TYR 0.026 0.002 TYR C1229 ARG 0.019 0.001 ARG C 974 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 449 time to evaluate : 3.930 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: A 142 MET cc_start: 0.6775 (pmm) cc_final: 0.5814 (pmm) REVERT: A 226 GLU cc_start: 0.8536 (tt0) cc_final: 0.8162 (tm-30) REVERT: B 205 MET cc_start: 0.8475 (tmm) cc_final: 0.8012 (tmm) REVERT: C 84 GLU cc_start: 0.7901 (mp0) cc_final: 0.7163 (mt-10) REVERT: C 133 ASN cc_start: 0.7744 (m-40) cc_final: 0.6838 (t0) REVERT: C 185 ASP cc_start: 0.7949 (t0) cc_final: 0.7117 (t0) REVERT: C 239 MET cc_start: 0.9419 (ppp) cc_final: 0.9206 (ppp) REVERT: C 429 MET cc_start: 0.9070 (mmm) cc_final: 0.8390 (mmm) REVERT: C 478 ARG cc_start: 0.8716 (mmp80) cc_final: 0.8441 (mmp80) REVERT: C 515 MET cc_start: 0.6882 (ttt) cc_final: 0.6566 (ttt) REVERT: C 704 MET cc_start: 0.8514 (tmm) cc_final: 0.8017 (tmm) REVERT: C 768 MET cc_start: 0.8176 (mtm) cc_final: 0.6959 (ptt) REVERT: C 813 GLU cc_start: 0.7954 (tp30) cc_final: 0.6945 (tt0) REVERT: C 878 THR cc_start: 0.7558 (p) cc_final: 0.7092 (t) REVERT: C 881 ASP cc_start: 0.8467 (t70) cc_final: 0.7968 (t0) REVERT: C 931 VAL cc_start: 0.9143 (t) cc_final: 0.8753 (m) REVERT: C 1119 MET cc_start: 0.8486 (tpp) cc_final: 0.8154 (tpp) REVERT: C 1178 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8430 (mmmt) REVERT: C 1232 MET cc_start: 0.7894 (mmm) cc_final: 0.6645 (mtp) REVERT: C 1272 GLU cc_start: 0.6644 (pt0) cc_final: 0.5568 (pt0) REVERT: C 1276 TRP cc_start: 0.8663 (m-10) cc_final: 0.7713 (m-90) REVERT: C 1290 MET cc_start: 0.7772 (tpp) cc_final: 0.6965 (tpp) REVERT: D 49 PHE cc_start: 0.7916 (m-80) cc_final: 0.7549 (m-80) REVERT: D 134 ASP cc_start: 0.8634 (t70) cc_final: 0.8422 (t0) REVERT: D 160 LEU cc_start: 0.8838 (mm) cc_final: 0.8351 (mm) REVERT: D 164 GLN cc_start: 0.9019 (mt0) cc_final: 0.8654 (mt0) REVERT: D 248 ASP cc_start: 0.8079 (m-30) cc_final: 0.7712 (t0) REVERT: D 282 LEU cc_start: 0.9249 (mt) cc_final: 0.8977 (tt) REVERT: D 330 MET cc_start: 0.6320 (mmt) cc_final: 0.5790 (mtp) REVERT: D 438 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7959 (mt-10) REVERT: D 478 LEU cc_start: 0.8570 (mt) cc_final: 0.8244 (mt) REVERT: D 479 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7191 (mt-10) REVERT: D 484 MET cc_start: 0.8076 (mpp) cc_final: 0.7619 (mpp) REVERT: D 485 MET cc_start: 0.7795 (ttp) cc_final: 0.6220 (ptp) REVERT: D 492 SER cc_start: 0.8059 (t) cc_final: 0.7752 (p) REVERT: D 569 LEU cc_start: 0.8978 (tp) cc_final: 0.8490 (mp) REVERT: D 625 MET cc_start: 0.7784 (tmm) cc_final: 0.7423 (tmm) REVERT: D 644 MET cc_start: 0.6957 (mpp) cc_final: 0.6639 (mpp) REVERT: D 697 MET cc_start: 0.7401 (tmm) cc_final: 0.7129 (tmm) REVERT: D 714 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7929 (mp0) REVERT: D 743 MET cc_start: 0.7287 (ptm) cc_final: 0.6879 (ptm) REVERT: D 1219 ASP cc_start: 0.9031 (t0) cc_final: 0.8665 (t0) REVERT: D 1345 ARG cc_start: 0.6976 (mmt90) cc_final: 0.6563 (mmt90) REVERT: D 1370 MET cc_start: 0.8110 (tpt) cc_final: 0.7757 (tpp) REVERT: F 74 ASP cc_start: 0.9147 (t0) cc_final: 0.8671 (t0) REVERT: F 91 TYR cc_start: 0.8542 (m-10) cc_final: 0.8133 (m-80) REVERT: F 113 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8005 (mm-30) REVERT: F 116 GLU cc_start: 0.8634 (pp20) cc_final: 0.8358 (pp20) REVERT: F 119 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7778 (pttt) REVERT: F 134 ASP cc_start: 0.8236 (t70) cc_final: 0.7964 (t0) REVERT: K 93 ASN cc_start: 0.8780 (t0) cc_final: 0.8386 (t0) REVERT: K 101 ARG cc_start: 0.8614 (ptp90) cc_final: 0.8299 (ptt-90) REVERT: E 29 GLN cc_start: 0.9464 (tt0) cc_final: 0.9023 (tt0) REVERT: E 42 GLU cc_start: 0.6809 (mp0) cc_final: 0.6472 (mp0) REVERT: E 60 ASN cc_start: 0.7735 (p0) cc_final: 0.7533 (p0) REVERT: E 67 ARG cc_start: 0.8954 (ttm110) cc_final: 0.8476 (mtm110) REVERT: G 1 MET cc_start: 0.9170 (ptm) cc_final: 0.8589 (ptm) REVERT: G 27 GLN cc_start: 0.8661 (pp30) cc_final: 0.8240 (pp30) REVERT: G 131 ARG cc_start: 0.9404 (ptt-90) cc_final: 0.9093 (ptp90) REVERT: H 1 MET cc_start: 0.7749 (ttt) cc_final: 0.7421 (ttt) REVERT: H 87 ARG cc_start: 0.9087 (ttm-80) cc_final: 0.8825 (ttt180) REVERT: H 184 MET cc_start: 0.5890 (mmm) cc_final: 0.5286 (mmm) REVERT: H 187 MET cc_start: 0.3493 (mtm) cc_final: 0.2323 (ttt) REVERT: I 1 MET cc_start: 0.7147 (ttm) cc_final: 0.6800 (ttt) REVERT: I 184 MET cc_start: 0.8583 (mmp) cc_final: 0.8310 (mmt) REVERT: I 187 MET cc_start: 0.7922 (tpt) cc_final: 0.6786 (tpt) REVERT: I 189 MET cc_start: 0.5576 (ptp) cc_final: 0.3893 (mtp) outliers start: 3 outliers final: 0 residues processed: 452 average time/residue: 0.4754 time to fit residues: 349.8441 Evaluate side-chains 354 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 241 optimal weight: 5.9990 chunk 389 optimal weight: 40.0000 chunk 237 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 270 optimal weight: 8.9990 chunk 408 optimal weight: 50.0000 chunk 375 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS C 41 GLN C 69 GLN C 649 GLN ** C 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN D 448 GLN ** D 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 34467 Z= 0.343 Angle : 0.711 12.127 46973 Z= 0.372 Chirality : 0.045 0.216 5376 Planarity : 0.005 0.099 5798 Dihedral : 16.304 123.582 5465 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.45 % Favored : 91.52 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -1.77 (0.13), residues: 4046 helix: 0.25 (0.14), residues: 1339 sheet: -1.29 (0.21), residues: 595 loop : -2.14 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 807 HIS 0.007 0.001 HIS C1237 PHE 0.021 0.002 PHE D 629 TYR 0.029 0.002 TYR C1229 ARG 0.016 0.001 ARG H 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8092 Ramachandran restraints generated. 4046 Oldfield, 0 Emsley, 4046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 433 time to evaluate : 4.532 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: A 77 ASP cc_start: 0.8590 (t0) cc_final: 0.8330 (m-30) REVERT: A 142 MET cc_start: 0.6780 (pmm) cc_final: 0.5854 (pmm) REVERT: A 205 MET cc_start: 0.6467 (pmm) cc_final: 0.6264 (pmm) REVERT: A 226 GLU cc_start: 0.8476 (tt0) cc_final: 0.8189 (tm-30) REVERT: B 205 MET cc_start: 0.8490 (tmm) cc_final: 0.7976 (tmm) REVERT: C 84 GLU cc_start: 0.7907 (mp0) cc_final: 0.7208 (mt-10) REVERT: C 133 ASN cc_start: 0.7669 (m-40) cc_final: 0.6955 (t0) REVERT: C 185 ASP cc_start: 0.7951 (t0) cc_final: 0.7149 (t0) REVERT: C 239 MET cc_start: 0.9443 (ppp) cc_final: 0.9230 (ppp) REVERT: C 429 MET cc_start: 0.9082 (mmm) cc_final: 0.8407 (mmm) REVERT: C 434 ASP cc_start: 0.8991 (m-30) cc_final: 0.8785 (m-30) REVERT: C 515 MET cc_start: 0.7067 (ttt) cc_final: 0.6775 (ttt) REVERT: C 704 MET cc_start: 0.8518 (tmm) cc_final: 0.7983 (tmm) REVERT: C 741 MET cc_start: 0.6582 (ptp) cc_final: 0.4639 (ptp) REVERT: C 768 MET cc_start: 0.8151 (mtm) cc_final: 0.7304 (ptt) REVERT: C 878 THR cc_start: 0.7495 (p) cc_final: 0.7028 (t) REVERT: C 931 VAL cc_start: 0.9164 (t) cc_final: 0.8823 (m) REVERT: C 1119 MET cc_start: 0.8509 (tpp) cc_final: 0.8189 (tpp) REVERT: C 1176 LEU cc_start: 0.9082 (mm) cc_final: 0.8856 (mm) REVERT: C 1178 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8402 (mmmt) REVERT: C 1232 MET cc_start: 0.7898 (mmm) cc_final: 0.6681 (mtp) REVERT: C 1272 GLU cc_start: 0.6688 (pt0) cc_final: 0.5608 (pt0) REVERT: C 1276 TRP cc_start: 0.8662 (m-10) cc_final: 0.7773 (m-90) REVERT: D 49 PHE cc_start: 0.7904 (m-80) cc_final: 0.7533 (m-80) REVERT: D 134 ASP cc_start: 0.8619 (t70) cc_final: 0.8320 (t0) REVERT: D 136 GLU cc_start: 0.8643 (tp30) cc_final: 0.8415 (tp30) REVERT: D 160 LEU cc_start: 0.8863 (mm) cc_final: 0.8599 (mm) REVERT: D 180 MET cc_start: 0.6767 (mtp) cc_final: 0.6324 (mtt) REVERT: D 248 ASP cc_start: 0.7995 (m-30) cc_final: 0.7623 (t0) REVERT: D 282 LEU cc_start: 0.9254 (mt) cc_final: 0.8970 (tt) REVERT: D 330 MET cc_start: 0.6331 (mmt) cc_final: 0.5835 (mtp) REVERT: D 438 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8012 (mt-10) REVERT: D 478 LEU cc_start: 0.8591 (mt) cc_final: 0.8279 (mt) REVERT: D 479 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7222 (mt-10) REVERT: D 484 MET cc_start: 0.8089 (mpp) cc_final: 0.7713 (mpp) REVERT: D 492 SER cc_start: 0.8185 (t) cc_final: 0.7829 (p) REVERT: D 513 MET cc_start: 0.8669 (ttp) cc_final: 0.8404 (ttp) REVERT: D 644 MET cc_start: 0.7388 (mpp) cc_final: 0.7148 (mpp) REVERT: D 697 MET cc_start: 0.7404 (tmm) cc_final: 0.7203 (tmm) REVERT: D 714 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7875 (mp0) REVERT: D 720 ASN cc_start: 0.8426 (t0) cc_final: 0.7941 (t0) REVERT: D 743 MET cc_start: 0.7289 (ptm) cc_final: 0.6900 (ptm) REVERT: D 1219 ASP cc_start: 0.9060 (t0) cc_final: 0.8682 (t0) REVERT: D 1345 ARG cc_start: 0.6968 (mmt90) cc_final: 0.6553 (mmt90) REVERT: D 1370 MET cc_start: 0.8123 (tpt) cc_final: 0.7753 (tpp) REVERT: F 74 ASP cc_start: 0.9217 (t0) cc_final: 0.8751 (t0) REVERT: F 91 TYR cc_start: 0.8600 (m-10) cc_final: 0.8209 (m-80) REVERT: F 113 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8060 (mm-30) REVERT: F 116 GLU cc_start: 0.8663 (pp20) cc_final: 0.8420 (pp20) REVERT: F 134 ASP cc_start: 0.8230 (t70) cc_final: 0.7977 (t0) REVERT: F 136 MET cc_start: 0.6801 (tpp) cc_final: 0.6414 (tpp) REVERT: K 93 ASN cc_start: 0.8825 (t0) cc_final: 0.8430 (t0) REVERT: K 101 ARG cc_start: 0.8555 (ptp90) cc_final: 0.8252 (ptt-90) REVERT: E 42 GLU cc_start: 0.6648 (mp0) cc_final: 0.6323 (mp0) REVERT: E 60 ASN cc_start: 0.7741 (p0) cc_final: 0.7534 (p0) REVERT: E 67 ARG cc_start: 0.8941 (ttm110) cc_final: 0.8581 (mtm110) REVERT: G 1 MET cc_start: 0.9191 (ptm) cc_final: 0.8586 (ptm) REVERT: G 27 GLN cc_start: 0.8609 (pp30) cc_final: 0.8207 (pp30) REVERT: G 131 ARG cc_start: 0.9417 (ptt-90) cc_final: 0.9107 (ptp90) REVERT: H 1 MET cc_start: 0.7655 (ttt) cc_final: 0.7359 (ttt) REVERT: H 87 ARG cc_start: 0.9085 (ttm-80) cc_final: 0.8826 (ttt180) REVERT: H 184 MET cc_start: 0.5855 (mmm) cc_final: 0.5247 (mmm) REVERT: H 187 MET cc_start: 0.3445 (mtm) cc_final: 0.2277 (ttt) REVERT: I 1 MET cc_start: 0.7143 (ttm) cc_final: 0.6789 (ttt) REVERT: I 184 MET cc_start: 0.8611 (mmp) cc_final: 0.8339 (mmt) REVERT: I 187 MET cc_start: 0.7939 (tpt) cc_final: 0.6813 (tpt) REVERT: I 189 MET cc_start: 0.5629 (ptp) cc_final: 0.3926 (mtp) outliers start: 2 outliers final: 1 residues processed: 435 average time/residue: 0.4853 time to fit residues: 346.3458 Evaluate side-chains 352 residues out of total 3462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 351 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 410 random chunks: chunk 258 optimal weight: 1.9990 chunk 346 optimal weight: 30.0000 chunk 99 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 334 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS C 69 GLN C 618 GLN C 649 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN F 85 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.135334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.114252 restraints weight = 92458.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114866 restraints weight = 205492.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.114775 restraints weight = 148530.924| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34467 Z= 0.250 Angle : 0.652 11.637 46973 Z= 0.341 Chirality : 0.044 0.219 5376 Planarity : 0.004 0.085 5798 Dihedral : 16.249 123.152 5465 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 0.09 % Allowed : 0.43 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % 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: -1.53 (0.13), residues: 4046 helix: 0.47 (0.14), residues: 1333 sheet: -1.03 (0.22), residues: 568 loop : -2.06 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 807 HIS 0.005 0.001 HIS C1237 PHE 0.017 0.001 PHE D 629 TYR 0.025 0.002 TYR A 177 ARG 0.011 0.001 ARG H 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7499.38 seconds wall clock time: 137 minutes 9.01 seconds (8229.01 seconds total)