Starting phenix.real_space_refine on Wed Mar 20 22:53:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkf_34851/03_2024/8hkf_34851.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkf_34851/03_2024/8hkf_34851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkf_34851/03_2024/8hkf_34851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkf_34851/03_2024/8hkf_34851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkf_34851/03_2024/8hkf_34851.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkf_34851/03_2024/8hkf_34851.pdb" } resolution = 2.66 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= 0.048 sd= 0.177 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: 6 Type Number sf(0) Gaussians K 16 8.98 5 Zn 4 6.06 5 S 212 5.16 5 C 18588 2.51 5 N 4772 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A ASP 843": "OD1" <-> "OD2" Residue "A GLU 860": "OE1" <-> "OE2" Residue "A TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 946": "OE1" <-> "OE2" Residue "A PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1187": "OD1" <-> "OD2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 631": "OE1" <-> "OE2" Residue "B GLU 791": "OE1" <-> "OE2" Residue "B GLU 808": "OE1" <-> "OE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B ASP 843": "OD1" <-> "OD2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 860": "OE1" <-> "OE2" Residue "B ASP 864": "OD1" <-> "OD2" Residue "B ASP 878": "OD1" <-> "OD2" Residue "B ASP 884": "OD1" <-> "OD2" Residue "B TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "B PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1151": "OE1" <-> "OE2" Residue "B ASP 1187": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "C GLU 630": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 791": "OE1" <-> "OE2" Residue "C GLU 830": "OE1" <-> "OE2" Residue "C ASP 878": "OD1" <-> "OD2" Residue "C ASP 884": "OD1" <-> "OD2" Residue "C TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 946": "OE1" <-> "OE2" Residue "C PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1151": "OE1" <-> "OE2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 574": "OE1" <-> "OE2" Residue "D GLU 576": "OE1" <-> "OE2" Residue "D TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 601": "OE1" <-> "OE2" Residue "D GLU 630": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D ASP 782": "OD1" <-> "OD2" Residue "D GLU 791": "OE1" <-> "OE2" Residue "D ASP 792": "OD1" <-> "OD2" Residue "D GLU 808": "OE1" <-> "OE2" Residue "D ASP 839": "OD1" <-> "OD2" Residue "D GLU 848": "OE1" <-> "OE2" Residue "D GLU 860": "OE1" <-> "OE2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D TYR 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 946": "OE1" <-> "OE2" Residue "D PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1151": "OE1" <-> "OE2" Residue "D ASP 1187": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28700 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 7170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7170 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 7, ' ZN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 3, ' ZN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A 777 94.964 62.616 128.258 1.00 76.38 S ATOM 4454 SG CYS A 778 98.806 62.321 128.069 1.00 80.73 S ATOM 4508 SG CYS A 785 97.164 65.665 128.995 1.00106.89 S ATOM 11618 SG CYS B 777 85.072 94.976 128.271 1.00 78.75 S ATOM 11624 SG CYS B 778 85.360 98.815 128.069 1.00 81.80 S ATOM 11678 SG CYS B 785 82.006 97.172 128.980 1.00108.36 S ATOM 18788 SG CYS C 777 52.631 85.104 128.346 1.00 76.11 S ATOM 18794 SG CYS C 778 48.797 85.346 128.094 1.00 82.44 S ATOM 18848 SG CYS C 785 50.465 81.992 128.989 1.00106.31 S ATOM 25958 SG CYS D 777 62.645 52.716 128.268 1.00 73.76 S ATOM 25964 SG CYS D 778 62.334 48.877 128.077 1.00 80.93 S ATOM 26018 SG CYS D 785 65.691 50.496 129.000 1.00108.52 S Time building chain proxies: 14.84, per 1000 atoms: 0.52 Number of scatterers: 28700 At special positions: 0 Unit cell: (148.72, 148.72, 142.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 K 16 19.00 S 212 16.00 O 5108 8.00 N 4772 7.00 C 18588 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: 10.73 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 778 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 778 " pdb=" ZN C1301 " pdb="ZN ZN C1301 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 778 " pdb=" ZN D1301 " pdb="ZN ZN D1301 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 778 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 785 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 20 sheets defined 54.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 110 through 137 Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 removed outlier: 3.625A pdb=" N ALA A 178 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Proline residue: A 221 - end of helix removed outlier: 3.844A pdb=" N ILE A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 256 removed outlier: 3.932A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 256 " --> pdb=" O MET A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix removed outlier: 3.506A pdb=" N GLU A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 422 through 427 removed outlier: 4.208A pdb=" N GLN A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.702A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.626A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.528A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.152A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.804A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 4.117A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.956A pdb=" N ASP A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1013 through 1017 removed outlier: 3.805A pdb=" N LEU A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.751A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 removed outlier: 3.696A pdb=" N ALA B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Proline residue: B 221 - end of helix removed outlier: 3.920A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Proline residue: B 230 - end of helix No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 256 removed outlier: 4.109A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 422 through 427 removed outlier: 4.192A pdb=" N GLN B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 463 through 482 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.702A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.621A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.518A pdb=" N ARG B 780 " --> pdb=" O CYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.525A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 823 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.813A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 4.124A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.912A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.736A pdb=" N LEU B1017 " --> pdb=" O GLU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.557A pdb=" N ALA C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 219 through 228 removed outlier: 3.541A pdb=" N ILE C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 256 removed outlier: 4.127A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 395 through 400 removed outlier: 6.757A pdb=" N ARG C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 422 through 427 removed outlier: 4.253A pdb=" N GLN C 427 " --> pdb=" O PRO C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.701A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 500 " --> pdb=" O LYS C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.626A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.620A pdb=" N ARG C 780 " --> pdb=" O CYS C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.538A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 823 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.814A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 4.129A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.957A pdb=" N ASP C 976 " --> pdb=" O ILE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1013 through 1017 removed outlier: 3.753A pdb=" N LEU C1017 " --> pdb=" O GLU C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 111 through 137 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 removed outlier: 3.818A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 226 through 227 No H-bonds generated for 'chain 'D' and resid 226 through 227' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 240 through 256 removed outlier: 4.067A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.763A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 422 through 427 removed outlier: 4.208A pdb=" N GLN D 427 " --> pdb=" O PRO D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.617A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 500 " --> pdb=" O LYS D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.629A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.507A pdb=" N ARG D 780 " --> pdb=" O CYS D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.531A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 822 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.149A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.815A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.135A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 removed outlier: 3.954A pdb=" N ASP D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1013 through 1017 removed outlier: 3.723A pdb=" N LEU D1017 " --> pdb=" O GLU D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.227A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.634A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.085A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 879 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.006A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.238A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.638A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AA9, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.101A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.991A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.228A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.638A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB5, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.112A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.984A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 433 removed outlier: 6.226A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.636A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC1, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.100A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN D 879 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.978A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 3981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.92 Time building geometry restraints manager: 11.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.15: 1 1.15 - 1.47: 16150 1.47 - 1.78: 12912 1.78 - 2.10: 280 2.10 - 2.41: 1 Bond restraints: 29344 Sorted by residual: bond pdb=" CG PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 1.503 0.840 0.663 3.40e-02 8.65e+02 3.80e+02 bond pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " ideal model delta sigma weight residual 1.492 2.412 -0.920 5.00e-02 4.00e+02 3.38e+02 bond pdb=" C ASP B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 1.336 1.559 -0.223 1.23e-02 6.61e+03 3.29e+02 bond pdb=" CG ARG C 232 " pdb=" CD ARG C 232 " ideal model delta sigma weight residual 1.520 1.287 0.233 3.00e-02 1.11e+03 6.04e+01 bond pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " ideal model delta sigma weight residual 1.808 1.586 0.222 3.30e-02 9.18e+02 4.55e+01 ... (remaining 29339 not shown) Histogram of bond angle deviations from ideal: 0.08 - 31.38: 1 31.38 - 62.69: 0 62.69 - 93.99: 8 93.99 - 125.29: 39322 125.29 - 156.60: 481 Bond angle restraints: 39812 Sorted by residual: angle pdb=" CB PRO B 139 " pdb=" CG PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 106.10 0.08 106.02 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO B 139 " pdb=" N PRO B 139 " pdb=" CD PRO B 139 " ideal model delta sigma weight residual 112.00 84.71 27.29 1.40e+00 5.10e-01 3.80e+02 angle pdb=" N TRP C 146 " pdb=" CA TRP C 146 " pdb=" C TRP C 146 " ideal model delta sigma weight residual 112.86 134.82 -21.96 1.22e+00 6.72e-01 3.24e+02 angle pdb=" N TRP D 146 " pdb=" CA TRP D 146 " pdb=" C TRP D 146 " ideal model delta sigma weight residual 112.86 134.20 -21.34 1.22e+00 6.72e-01 3.06e+02 angle pdb=" C TRP D 146 " pdb=" CA TRP D 146 " pdb=" CB TRP D 146 " ideal model delta sigma weight residual 111.36 83.74 27.62 1.63e+00 3.76e-01 2.87e+02 ... (remaining 39807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 15898 20.44 - 40.88: 1353 40.88 - 61.32: 283 61.32 - 81.76: 49 81.76 - 102.20: 21 Dihedral angle restraints: 17604 sinusoidal: 6992 harmonic: 10612 Sorted by residual: dihedral pdb=" N PRO A 149 " pdb=" C PRO A 149 " pdb=" CA PRO A 149 " pdb=" CB PRO A 149 " ideal model delta harmonic sigma weight residual 115.10 134.13 -19.03 0 2.50e+00 1.60e-01 5.80e+01 dihedral pdb=" C PRO A 149 " pdb=" N PRO A 149 " pdb=" CA PRO A 149 " pdb=" CB PRO A 149 " ideal model delta harmonic sigma weight residual -120.70 -139.50 18.80 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" C TRP D 146 " pdb=" N TRP D 146 " pdb=" CA TRP D 146 " pdb=" CB TRP D 146 " ideal model delta harmonic sigma weight residual -122.60 -104.45 -18.15 0 2.50e+00 1.60e-01 5.27e+01 ... (remaining 17601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 4533 0.206 - 0.413: 10 0.413 - 0.619: 2 0.619 - 0.826: 2 0.826 - 1.032: 1 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CA PRO A 149 " pdb=" N PRO A 149 " pdb=" C PRO A 149 " pdb=" CB PRO A 149 " both_signs ideal model delta sigma weight residual False 2.72 1.69 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA PRO C 149 " pdb=" N PRO C 149 " pdb=" C PRO C 149 " pdb=" CB PRO C 149 " both_signs ideal model delta sigma weight residual False 2.72 1.91 0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 2.01 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4545 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 177 " 0.058 2.00e-02 2.50e+03 4.63e-02 5.35e+01 pdb=" CG TRP C 177 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP C 177 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C 177 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 177 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP C 177 " -0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 177 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 177 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 177 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 148 " 0.095 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO C 149 " -0.247 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 148 " 0.095 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO D 149 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " 0.074 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.22: 37 2.22 - 2.95: 12771 2.95 - 3.68: 50387 3.68 - 4.41: 86113 4.41 - 5.14: 141623 Nonbonded interactions: 290931 Sorted by model distance: nonbonded pdb=" O TRP C 146 " pdb=" CD1 TRP C 146 " model vdw 1.494 3.260 nonbonded pdb=" O TRP C 146 " pdb=" CG TRP C 146 " model vdw 1.558 3.260 nonbonded pdb=" CD1 LEU B 802 " pdb=" CE1 TYR B 876 " model vdw 1.787 3.760 nonbonded pdb=" O TRP D 146 " pdb=" CG TRP D 146 " model vdw 1.806 3.260 nonbonded pdb=" CD1 LEU D 802 " pdb=" CE1 TYR D 876 " model vdw 1.820 3.760 ... (remaining 290926 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 110 through 1205 or resid 1301 through 1304)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 5.120 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 79.940 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 0.920 29344 Z= 0.577 Angle : 0.967 106.020 39812 Z= 0.484 Chirality : 0.050 1.032 4548 Planarity : 0.006 0.143 4992 Dihedral : 16.149 102.196 10716 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 0.60 % Allowed : 22.14 % Favored : 77.26 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 3532 helix: -0.01 (0.12), residues: 1684 sheet: -0.37 (0.25), residues: 364 loop : -0.41 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.002 TRP C 177 HIS 0.010 0.001 HIS C 291 PHE 0.035 0.002 PHE A 188 TYR 0.018 0.001 TYR C 403 ARG 0.013 0.001 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 552 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7781 (ttt90) REVERT: B 168 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7833 (tt) REVERT: B 294 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8165 (ttp80) REVERT: B 398 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7714 (ttt90) REVERT: C 950 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7337 (ttp80) REVERT: D 783 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7740 (pttp) REVERT: D 786 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8273 (mppt) REVERT: D 1018 TRP cc_start: 0.8221 (p-90) cc_final: 0.7967 (p-90) outliers start: 19 outliers final: 13 residues processed: 567 average time/residue: 1.3162 time to fit residues: 874.4492 Evaluate side-chains 536 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 522 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 925 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.9990 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 182 optimal weight: 40.0000 chunk 144 optimal weight: 0.9980 chunk 279 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 298 ASN A 470 GLN A 505 HIS A 535 HIS A 632 ASN A 816 ASN ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 270 GLN B 470 GLN B 505 HIS B 535 HIS B 632 ASN B 816 ASN B 845 HIS ** B1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 357 GLN C 470 GLN C 505 HIS C 614 HIS C 632 ASN C 816 ASN C1175 ASN D 156 ASN D 218 ASN D 251 ASN D 470 GLN D 505 HIS D 535 HIS D 614 HIS D 632 ASN D 816 ASN D 845 HIS ** D1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 29344 Z= 0.252 Angle : 0.608 11.097 39812 Z= 0.305 Chirality : 0.043 0.310 4548 Planarity : 0.006 0.160 4992 Dihedral : 4.928 58.253 3921 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 3.62 % Allowed : 19.98 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3532 helix: 0.80 (0.12), residues: 1668 sheet: -0.29 (0.25), residues: 388 loop : -0.04 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 177 HIS 0.005 0.001 HIS A1046 PHE 0.020 0.002 PHE B 188 TYR 0.018 0.001 TYR B 403 ARG 0.006 0.001 ARG D1143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 544 time to evaluate : 3.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8520 (p) cc_final: 0.8209 (m) REVERT: A 174 MET cc_start: 0.7012 (tpt) cc_final: 0.6618 (tpp) REVERT: A 200 LYS cc_start: 0.3700 (OUTLIER) cc_final: 0.3378 (ttpp) REVERT: A 267 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: A 334 MET cc_start: 0.8132 (tpp) cc_final: 0.7841 (mmt) REVERT: A 398 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7713 (ttt90) REVERT: A 783 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7383 (pttp) REVERT: A 788 ASN cc_start: 0.7702 (p0) cc_final: 0.7411 (p0) REVERT: A 791 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: A 974 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8169 (tmm) REVERT: B 168 LEU cc_start: 0.8137 (tp) cc_final: 0.7904 (tt) REVERT: B 200 LYS cc_start: 0.3334 (OUTLIER) cc_final: 0.3120 (tttt) REVERT: B 371 GLU cc_start: 0.6313 (mp0) cc_final: 0.6106 (mp0) REVERT: B 398 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7715 (ttt90) REVERT: B 538 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7152 (mmp80) REVERT: B 845 HIS cc_start: 0.7695 (m-70) cc_final: 0.7433 (m170) REVERT: C 190 GLU cc_start: 0.7232 (mp0) cc_final: 0.6736 (mp0) REVERT: C 538 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7099 (mmp80) REVERT: C 788 ASN cc_start: 0.7851 (p0) cc_final: 0.7534 (p0) REVERT: C 930 MET cc_start: 0.7130 (tpt) cc_final: 0.6878 (tpt) REVERT: C 1158 LYS cc_start: 0.8232 (mttt) cc_final: 0.7957 (mtmp) REVERT: D 117 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7224 (mm) REVERT: D 192 MET cc_start: 0.5880 (mtp) cc_final: 0.5484 (mtt) REVERT: D 538 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7142 (mmp80) REVERT: D 604 LYS cc_start: 0.7960 (pttt) cc_final: 0.7739 (pptt) REVERT: D 786 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8181 (mppt) REVERT: D 829 LYS cc_start: 0.7589 (tmtt) cc_final: 0.7288 (tptp) REVERT: D 830 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: D 950 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7576 (ttp80) REVERT: D 974 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8128 (tmm) REVERT: D 1152 LEU cc_start: 0.8572 (tp) cc_final: 0.8367 (tp) outliers start: 114 outliers final: 32 residues processed: 598 average time/residue: 1.3143 time to fit residues: 923.6141 Evaluate side-chains 564 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 519 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 PRO Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain C residue 149 PRO Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 384 ASP Chi-restraints excluded: chain C residue 538 ARG Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 974 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 220 optimal weight: 1.9990 chunk 89 optimal weight: 30.0000 chunk 323 optimal weight: 0.8980 chunk 349 optimal weight: 7.9990 chunk 288 optimal weight: 3.9990 chunk 321 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 HIS B 632 ASN B1175 ASN C 156 ASN C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 369 GLN C 632 ASN D 156 ASN D 251 ASN D 632 ASN D 845 HIS D1175 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 29344 Z= 0.471 Angle : 0.678 9.843 39812 Z= 0.337 Chirality : 0.048 0.310 4548 Planarity : 0.006 0.153 4992 Dihedral : 5.105 54.420 3913 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 5.02 % Allowed : 19.35 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3532 helix: 0.72 (0.12), residues: 1696 sheet: -0.30 (0.25), residues: 388 loop : -0.09 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 177 HIS 0.007 0.002 HIS C 586 PHE 0.026 0.002 PHE D 283 TYR 0.035 0.002 TYR D 876 ARG 0.009 0.001 ARG B 948 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 557 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8481 (p) cc_final: 0.8094 (m) REVERT: A 200 LYS cc_start: 0.3744 (OUTLIER) cc_final: 0.3335 (ttpp) REVERT: A 312 PHE cc_start: 0.8691 (m-80) cc_final: 0.8488 (m-80) REVERT: A 355 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: A 398 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7728 (ttt90) REVERT: A 538 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7135 (mmp80) REVERT: A 829 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8213 (mmtm) REVERT: A 968 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7830 (mmp80) REVERT: A 1137 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6995 (ttt-90) REVERT: B 200 LYS cc_start: 0.3590 (OUTLIER) cc_final: 0.3318 (tttt) REVERT: B 538 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7118 (mmp80) REVERT: B 565 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7174 (ttp-170) REVERT: B 788 ASN cc_start: 0.7934 (p0) cc_final: 0.7681 (p0) REVERT: B 968 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7885 (mmp80) REVERT: B 1140 LEU cc_start: 0.8235 (tp) cc_final: 0.7908 (tp) REVERT: C 180 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: C 346 PHE cc_start: 0.7353 (m-10) cc_final: 0.7104 (m-10) REVERT: C 788 ASN cc_start: 0.7951 (p0) cc_final: 0.7645 (p0) REVERT: C 968 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7848 (mmp80) REVERT: C 1158 LYS cc_start: 0.8157 (mttt) cc_final: 0.7933 (mtmp) REVERT: D 117 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7280 (mm) REVERT: D 128 LEU cc_start: 0.8016 (tm) cc_final: 0.7813 (OUTLIER) REVERT: D 538 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7161 (mmp80) REVERT: D 786 LYS cc_start: 0.8503 (mmtt) cc_final: 0.8193 (mppt) REVERT: D 830 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: D 968 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7885 (mmp80) REVERT: D 1158 LYS cc_start: 0.7983 (mtmp) cc_final: 0.7708 (mtmm) outliers start: 158 outliers final: 71 residues processed: 645 average time/residue: 1.3266 time to fit residues: 1004.6206 Evaluate side-chains 615 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 530 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 629 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1137 ARG Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 629 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 968 ARG Chi-restraints excluded: chain B residue 1038 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 629 LYS Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 968 ARG Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain C residue 1140 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 ASP Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 968 ARG Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 1038 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 168 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 325 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 308 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 298 ASN A 632 ASN A 845 HIS ** A1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS C 156 ASN C 251 ASN C 632 ASN C 845 HIS D 156 ASN D 251 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 29344 Z= 0.193 Angle : 0.569 11.423 39812 Z= 0.280 Chirality : 0.042 0.291 4548 Planarity : 0.005 0.145 4992 Dihedral : 4.803 58.056 3913 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.59 % Rotamer: Outliers : 3.40 % Allowed : 20.87 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3532 helix: 1.22 (0.13), residues: 1676 sheet: -0.36 (0.26), residues: 396 loop : 0.15 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 177 HIS 0.005 0.001 HIS C 291 PHE 0.024 0.001 PHE B 283 TYR 0.022 0.001 TYR D 553 ARG 0.008 0.000 ARG C 948 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 544 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8459 (tp40) cc_final: 0.8162 (tp40) REVERT: A 351 TYR cc_start: 0.6708 (t80) cc_final: 0.6460 (t80) REVERT: A 398 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7713 (ttt90) REVERT: A 426 SER cc_start: 0.8813 (t) cc_final: 0.8337 (p) REVERT: A 538 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7102 (mmp80) REVERT: A 565 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7882 (ttt90) REVERT: A 788 ASN cc_start: 0.7640 (p0) cc_final: 0.7383 (p0) REVERT: A 791 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: A 829 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8186 (mmtm) REVERT: A 1158 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7760 (mtmm) REVERT: B 168 LEU cc_start: 0.8129 (tp) cc_final: 0.7881 (tt) REVERT: B 200 LYS cc_start: 0.3277 (OUTLIER) cc_final: 0.3065 (tttt) REVERT: B 398 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7927 (ttt180) REVERT: B 538 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7117 (mmp80) REVERT: B 565 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7013 (ttp-170) REVERT: B 788 ASN cc_start: 0.7799 (p0) cc_final: 0.7582 (p0) REVERT: B 829 LYS cc_start: 0.8452 (mttt) cc_final: 0.8034 (tmtt) REVERT: B 830 GLU cc_start: 0.8159 (mp0) cc_final: 0.7687 (mp0) REVERT: B 859 MET cc_start: 0.8426 (ttm) cc_final: 0.8124 (ttm) REVERT: B 1140 LEU cc_start: 0.8071 (tp) cc_final: 0.7821 (tp) REVERT: C 170 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8260 (m) REVERT: C 180 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: C 312 PHE cc_start: 0.8908 (m-80) cc_final: 0.8614 (m-80) REVERT: C 346 PHE cc_start: 0.7352 (m-10) cc_final: 0.7099 (m-10) REVERT: C 565 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7690 (ttt90) REVERT: C 788 ASN cc_start: 0.7800 (p0) cc_final: 0.7519 (p0) REVERT: C 828 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7502 (ttm-80) REVERT: C 829 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8207 (mmpt) REVERT: C 930 MET cc_start: 0.6993 (tpt) cc_final: 0.6660 (tpt) REVERT: D 117 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7183 (mm) REVERT: D 128 LEU cc_start: 0.7978 (tm) cc_final: 0.7774 (tt) REVERT: D 604 LYS cc_start: 0.7947 (pttt) cc_final: 0.7705 (pptt) REVERT: D 629 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6877 (tttp) REVERT: D 786 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8182 (mppt) REVERT: D 830 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.8015 (mm-30) outliers start: 107 outliers final: 37 residues processed: 604 average time/residue: 1.3177 time to fit residues: 936.2857 Evaluate side-chains 568 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 519 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A1175 ASN B 632 ASN B 931 GLN C 156 ASN C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS C 632 ASN C1147 GLN D 156 ASN D 251 ASN D 632 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 29344 Z= 0.472 Angle : 0.693 10.349 39812 Z= 0.341 Chirality : 0.048 0.304 4548 Planarity : 0.006 0.141 4992 Dihedral : 5.105 49.936 3913 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 4.70 % Allowed : 21.32 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3532 helix: 0.97 (0.12), residues: 1720 sheet: -0.33 (0.26), residues: 388 loop : -0.09 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 177 HIS 0.008 0.002 HIS B 586 PHE 0.037 0.003 PHE C 188 TYR 0.021 0.002 TYR C 403 ARG 0.010 0.001 ARG C1143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 544 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7790 (ttt90) REVERT: A 426 SER cc_start: 0.8809 (t) cc_final: 0.8382 (p) REVERT: A 538 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7102 (mmt90) REVERT: A 565 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8071 (ttt90) REVERT: A 783 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7318 (pttp) REVERT: A 788 ASN cc_start: 0.7826 (p0) cc_final: 0.7548 (p0) REVERT: A 791 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: A 968 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7810 (mmp80) REVERT: A 1018 TRP cc_start: 0.8119 (p-90) cc_final: 0.7800 (p-90) REVERT: A 1137 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7465 (mtp180) REVERT: B 168 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7860 (tt) REVERT: B 200 LYS cc_start: 0.3272 (OUTLIER) cc_final: 0.3038 (tttt) REVERT: B 538 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7122 (mmp80) REVERT: B 565 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7208 (ttp-170) REVERT: B 788 ASN cc_start: 0.7958 (p0) cc_final: 0.7714 (p0) REVERT: B 1140 LEU cc_start: 0.8140 (tp) cc_final: 0.7890 (tp) REVERT: C 170 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8243 (m) REVERT: C 180 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: C 346 PHE cc_start: 0.7463 (m-10) cc_final: 0.7198 (m-10) REVERT: C 348 GLU cc_start: 0.7697 (tp30) cc_final: 0.7313 (tp30) REVERT: C 538 ARG cc_start: 0.7637 (mmt90) cc_final: 0.7396 (mmp80) REVERT: C 788 ASN cc_start: 0.7915 (p0) cc_final: 0.7601 (p0) REVERT: C 828 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7494 (ttm-80) REVERT: C 829 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8216 (mmpt) REVERT: D 117 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7247 (mm) REVERT: D 128 LEU cc_start: 0.8222 (tm) cc_final: 0.7994 (OUTLIER) REVERT: D 308 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8032 (m) REVERT: D 426 SER cc_start: 0.8761 (t) cc_final: 0.8410 (p) REVERT: D 538 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7150 (mmp80) REVERT: D 786 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8131 (mppt) REVERT: D 830 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: D 1158 LYS cc_start: 0.7955 (mttt) cc_final: 0.7554 (mtmp) outliers start: 148 outliers final: 76 residues processed: 622 average time/residue: 1.2929 time to fit residues: 949.6956 Evaluate side-chains 617 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 527 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1143 ARG Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 894 ASP Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 1038 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 ASP Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 0.7980 chunk 309 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 344 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 chunk 159 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 632 ASN A 845 HIS B 180 GLN B 218 ASN B 241 ASN B 632 ASN B 845 HIS B1147 GLN C 156 ASN C 251 ASN C 632 ASN C 845 HIS D 156 ASN D 251 ASN D 298 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 29344 Z= 0.192 Angle : 0.576 10.461 39812 Z= 0.282 Chirality : 0.042 0.262 4548 Planarity : 0.005 0.138 4992 Dihedral : 4.790 53.937 3913 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.76 % Rotamer: Outliers : 3.43 % Allowed : 22.40 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3532 helix: 1.35 (0.13), residues: 1684 sheet: -0.19 (0.29), residues: 340 loop : 0.12 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 177 HIS 0.004 0.001 HIS C 291 PHE 0.027 0.001 PHE B 283 TYR 0.021 0.001 TYR D 553 ARG 0.012 0.000 ARG C 948 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 532 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8297 (mmtt) REVERT: A 398 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7917 (ttt180) REVERT: A 426 SER cc_start: 0.8806 (t) cc_final: 0.8367 (p) REVERT: A 565 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7943 (ttt90) REVERT: A 783 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7420 (pttp) REVERT: A 788 ASN cc_start: 0.7675 (p0) cc_final: 0.7416 (p0) REVERT: A 829 LYS cc_start: 0.8451 (mmmt) cc_final: 0.8143 (mmtm) REVERT: A 1137 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7437 (mtp180) REVERT: B 168 LEU cc_start: 0.8201 (tp) cc_final: 0.7956 (tt) REVERT: B 200 LYS cc_start: 0.3289 (OUTLIER) cc_final: 0.3070 (tttt) REVERT: B 538 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7130 (mmp80) REVERT: B 565 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7058 (ttp-170) REVERT: B 788 ASN cc_start: 0.7801 (p0) cc_final: 0.7596 (p0) REVERT: B 892 GLU cc_start: 0.6198 (tm-30) cc_final: 0.5711 (pp20) REVERT: B 1140 LEU cc_start: 0.8052 (tp) cc_final: 0.7851 (tp) REVERT: C 170 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8201 (m) REVERT: C 180 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7457 (mt0) REVERT: C 193 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5907 (mt) REVERT: C 224 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7332 (tt) REVERT: C 252 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.6333 (mmt) REVERT: C 346 PHE cc_start: 0.7443 (m-10) cc_final: 0.7190 (m-10) REVERT: C 348 GLU cc_start: 0.7699 (tp30) cc_final: 0.7434 (tp30) REVERT: C 565 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7811 (ttp80) REVERT: C 788 ASN cc_start: 0.7853 (p0) cc_final: 0.7569 (p0) REVERT: C 828 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7479 (ttm-80) REVERT: C 829 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8175 (mmpt) REVERT: D 117 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7234 (mm) REVERT: D 124 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7983 (mm) REVERT: D 128 LEU cc_start: 0.8166 (tm) cc_final: 0.7950 (tt) REVERT: D 180 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7826 (tp40) REVERT: D 308 CYS cc_start: 0.8211 (OUTLIER) cc_final: 0.8004 (m) REVERT: D 426 SER cc_start: 0.8702 (t) cc_final: 0.8321 (p) REVERT: D 786 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8138 (mppt) REVERT: D 892 GLU cc_start: 0.6363 (tm-30) cc_final: 0.5911 (pp20) outliers start: 108 outliers final: 52 residues processed: 592 average time/residue: 1.3120 time to fit residues: 913.8557 Evaluate side-chains 597 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 529 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 629 LYS Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 289 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 343 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 632 ASN A 845 HIS A 931 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS D 156 ASN D 251 ASN D 632 ASN D 845 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 29344 Z= 0.344 Angle : 0.639 12.901 39812 Z= 0.310 Chirality : 0.045 0.272 4548 Planarity : 0.006 0.135 4992 Dihedral : 4.863 47.063 3913 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 3.81 % Allowed : 22.59 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3532 helix: 1.24 (0.12), residues: 1712 sheet: -0.30 (0.29), residues: 344 loop : -0.00 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 177 HIS 0.006 0.002 HIS C 586 PHE 0.041 0.002 PHE C 188 TYR 0.017 0.002 TYR B 403 ARG 0.012 0.001 ARG A 948 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 535 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8529 (p) cc_final: 0.8134 (m) REVERT: A 180 GLN cc_start: 0.8324 (tp40) cc_final: 0.8063 (tp40) REVERT: A 347 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: A 355 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: A 382 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8284 (mmtt) REVERT: A 398 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7790 (ttt90) REVERT: A 426 SER cc_start: 0.8793 (t) cc_final: 0.8359 (p) REVERT: A 538 ARG cc_start: 0.7622 (mmt90) cc_final: 0.7392 (mmp80) REVERT: A 565 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7986 (ttt90) REVERT: A 783 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7326 (pttp) REVERT: A 788 ASN cc_start: 0.7781 (p0) cc_final: 0.7503 (p0) REVERT: A 1137 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7453 (mtp180) REVERT: B 128 LEU cc_start: 0.7827 (tm) cc_final: 0.7611 (tt) REVERT: B 174 MET cc_start: 0.6577 (tpp) cc_final: 0.6164 (tpp) REVERT: B 200 LYS cc_start: 0.3263 (OUTLIER) cc_final: 0.3031 (tttt) REVERT: B 538 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7154 (mmp80) REVERT: B 565 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7071 (ttp-170) REVERT: B 788 ASN cc_start: 0.7860 (p0) cc_final: 0.7651 (p0) REVERT: B 892 GLU cc_start: 0.6259 (tm-30) cc_final: 0.5816 (pp20) REVERT: B 1140 LEU cc_start: 0.8050 (tp) cc_final: 0.7833 (tp) REVERT: C 170 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8190 (m) REVERT: C 180 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: C 193 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5878 (mt) REVERT: C 224 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7383 (tt) REVERT: C 252 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6372 (mtt) REVERT: C 346 PHE cc_start: 0.7474 (m-10) cc_final: 0.7211 (m-10) REVERT: C 348 GLU cc_start: 0.7709 (tp30) cc_final: 0.7459 (tp30) REVERT: C 565 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7846 (ttp80) REVERT: C 788 ASN cc_start: 0.7902 (p0) cc_final: 0.7614 (p0) REVERT: C 828 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7452 (ttm-80) REVERT: C 829 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8146 (mmpt) REVERT: D 117 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7314 (mm) REVERT: D 128 LEU cc_start: 0.8215 (tm) cc_final: 0.7964 (tp) REVERT: D 180 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7860 (tp40) REVERT: D 308 CYS cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (m) REVERT: D 426 SER cc_start: 0.8725 (t) cc_final: 0.8354 (p) REVERT: D 538 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7154 (mmp80) REVERT: D 786 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8137 (mppt) REVERT: D 830 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 892 GLU cc_start: 0.6393 (tm-30) cc_final: 0.5949 (pp20) REVERT: D 944 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7617 (mmtt) outliers start: 120 outliers final: 72 residues processed: 606 average time/residue: 1.2988 time to fit residues: 925.2345 Evaluate side-chains 616 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 525 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 427 GLN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 427 GLN Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 944 LYS Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 269 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 845 HIS A1147 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS C 251 ASN ** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS C 931 GLN D 156 ASN D 251 ASN D 845 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 29344 Z= 0.256 Angle : 0.611 14.352 39812 Z= 0.294 Chirality : 0.043 0.254 4548 Planarity : 0.005 0.133 4992 Dihedral : 4.675 36.800 3909 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.40 % Allowed : 22.68 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3532 helix: 1.38 (0.13), residues: 1688 sheet: -0.25 (0.29), residues: 344 loop : 0.14 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 177 HIS 0.008 0.001 HIS C 291 PHE 0.027 0.002 PHE B 283 TYR 0.017 0.002 TYR B 553 ARG 0.014 0.001 ARG A 948 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 525 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 VAL cc_start: 0.8537 (p) cc_final: 0.8168 (m) REVERT: A 180 GLN cc_start: 0.8337 (tp40) cc_final: 0.8066 (tp40) REVERT: A 347 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6562 (mm-30) REVERT: A 355 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 382 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8294 (mmtt) REVERT: A 398 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7765 (ttt90) REVERT: A 426 SER cc_start: 0.8775 (t) cc_final: 0.8341 (p) REVERT: A 538 ARG cc_start: 0.7625 (mmt90) cc_final: 0.7405 (mmp80) REVERT: A 565 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7960 (ttt90) REVERT: A 783 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7381 (pttp) REVERT: A 788 ASN cc_start: 0.7738 (p0) cc_final: 0.7473 (p0) REVERT: A 829 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8131 (mmtm) REVERT: A 892 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6189 (pp20) REVERT: A 1137 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7437 (mtp180) REVERT: B 128 LEU cc_start: 0.7824 (tm) cc_final: 0.7613 (tt) REVERT: B 174 MET cc_start: 0.6686 (tpp) cc_final: 0.6288 (tpp) REVERT: B 200 LYS cc_start: 0.3152 (OUTLIER) cc_final: 0.2932 (tttt) REVERT: B 538 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7157 (mmp80) REVERT: B 565 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7072 (ttp-170) REVERT: B 788 ASN cc_start: 0.7856 (p0) cc_final: 0.7644 (p0) REVERT: B 841 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8309 (tptp) REVERT: B 892 GLU cc_start: 0.6272 (tm-30) cc_final: 0.5876 (pp20) REVERT: C 170 VAL cc_start: 0.8544 (p) cc_final: 0.8128 (m) REVERT: C 180 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: C 193 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5858 (mt) REVERT: C 291 HIS cc_start: 0.8307 (t70) cc_final: 0.8085 (t-90) REVERT: C 346 PHE cc_start: 0.7445 (m-10) cc_final: 0.7178 (m-10) REVERT: C 348 GLU cc_start: 0.7725 (tp30) cc_final: 0.7492 (tp30) REVERT: C 565 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7796 (ttt90) REVERT: C 788 ASN cc_start: 0.7835 (p0) cc_final: 0.7549 (p0) REVERT: C 828 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7478 (ttm-80) REVERT: C 829 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8141 (mmpt) REVERT: C 859 MET cc_start: 0.8526 (ttm) cc_final: 0.8322 (ttm) REVERT: C 876 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: D 128 LEU cc_start: 0.8308 (tm) cc_final: 0.8052 (tp) REVERT: D 180 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7893 (tp40) REVERT: D 193 LEU cc_start: 0.5494 (OUTLIER) cc_final: 0.4638 (mt) REVERT: D 308 CYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7990 (m) REVERT: D 426 SER cc_start: 0.8729 (t) cc_final: 0.8348 (p) REVERT: D 538 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7161 (mmp80) REVERT: D 565 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7085 (ttp-170) REVERT: D 786 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8131 (mppt) REVERT: D 892 GLU cc_start: 0.6355 (tm-30) cc_final: 0.5986 (pp20) REVERT: D 944 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7602 (mmtt) outliers start: 107 outliers final: 66 residues processed: 593 average time/residue: 1.3469 time to fit residues: 937.5077 Evaluate side-chains 606 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 521 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 538 ARG Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 602 ASP Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 538 ARG Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 925 SER Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 944 LYS Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.8980 chunk 328 optimal weight: 0.3980 chunk 299 optimal weight: 1.9990 chunk 319 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 251 optimal weight: 6.9990 chunk 98 optimal weight: 0.0170 chunk 288 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 chunk 318 optimal weight: 10.0000 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 845 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS B1147 GLN ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 156 ASN D 251 ASN D 845 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 29344 Z= 0.180 Angle : 0.595 14.229 39812 Z= 0.284 Chirality : 0.041 0.245 4548 Planarity : 0.005 0.130 4992 Dihedral : 4.459 32.267 3909 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.49 % Favored : 97.42 % Rotamer: Outliers : 2.51 % Allowed : 23.60 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.14), residues: 3532 helix: 1.50 (0.13), residues: 1688 sheet: -0.03 (0.29), residues: 340 loop : 0.20 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP C 177 HIS 0.006 0.001 HIS C 291 PHE 0.035 0.001 PHE C 188 TYR 0.020 0.001 TYR D 553 ARG 0.013 0.000 ARG B 948 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 530 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8348 (tp40) cc_final: 0.8088 (tp40) REVERT: A 347 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6556 (mm-30) REVERT: A 355 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 382 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8309 (mmtt) REVERT: A 398 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7918 (ttt180) REVERT: A 426 SER cc_start: 0.8751 (t) cc_final: 0.8321 (p) REVERT: A 565 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7890 (ttt90) REVERT: A 783 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7315 (pttp) REVERT: A 788 ASN cc_start: 0.7610 (p0) cc_final: 0.7402 (p0) REVERT: A 829 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8208 (mmtm) REVERT: A 892 GLU cc_start: 0.6638 (tm-30) cc_final: 0.6252 (pp20) REVERT: A 1137 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7384 (mtp180) REVERT: B 128 LEU cc_start: 0.7861 (tm) cc_final: 0.7655 (tt) REVERT: B 565 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7022 (ttp-170) REVERT: B 892 GLU cc_start: 0.6232 (tm-30) cc_final: 0.5838 (pp20) REVERT: B 1158 LYS cc_start: 0.7961 (mtmp) cc_final: 0.7695 (mtmm) REVERT: C 133 ARG cc_start: 0.7794 (tmm-80) cc_final: 0.7541 (tmm160) REVERT: C 170 VAL cc_start: 0.8427 (p) cc_final: 0.7979 (m) REVERT: C 180 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: C 190 GLU cc_start: 0.7357 (mp0) cc_final: 0.6971 (mp0) REVERT: C 346 PHE cc_start: 0.7438 (m-10) cc_final: 0.7188 (m-10) REVERT: C 565 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7772 (ttt90) REVERT: C 788 ASN cc_start: 0.7774 (p0) cc_final: 0.7530 (p0) REVERT: C 829 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8158 (mmpt) REVERT: C 876 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: D 128 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8071 (tt) REVERT: D 180 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7867 (tp40) REVERT: D 192 MET cc_start: 0.5777 (mtp) cc_final: 0.5355 (mpp) REVERT: D 308 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7956 (m) REVERT: D 354 MET cc_start: 0.7278 (mtp) cc_final: 0.7019 (mtt) REVERT: D 426 SER cc_start: 0.8679 (t) cc_final: 0.8285 (p) REVERT: D 786 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8167 (mppt) REVERT: D 892 GLU cc_start: 0.6416 (tm-30) cc_final: 0.6059 (pp20) REVERT: D 1142 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6798 (mtp180) outliers start: 79 outliers final: 52 residues processed: 584 average time/residue: 1.3551 time to fit residues: 929.2826 Evaluate side-chains 590 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 526 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 568 ASP Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 354 optimal weight: 0.0050 chunk 326 optimal weight: 0.6980 chunk 282 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 218 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 845 HIS ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS B1147 GLN ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 291 HIS C 632 ASN C 845 HIS D 156 ASN D 251 ASN D 845 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 29344 Z= 0.183 Angle : 0.609 14.858 39812 Z= 0.287 Chirality : 0.042 0.243 4548 Planarity : 0.005 0.128 4992 Dihedral : 4.412 33.077 3909 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Rotamer: Outliers : 2.29 % Allowed : 24.40 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.14), residues: 3532 helix: 1.57 (0.13), residues: 1688 sheet: 0.02 (0.30), residues: 340 loop : 0.24 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 177 HIS 0.005 0.001 HIS B1046 PHE 0.029 0.001 PHE B 283 TYR 0.019 0.001 TYR D 553 ARG 0.014 0.001 ARG A 948 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 529 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8358 (tp40) cc_final: 0.8097 (tp40) REVERT: A 347 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6534 (mm-30) REVERT: A 382 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8367 (mmtm) REVERT: A 398 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7923 (ttt180) REVERT: A 426 SER cc_start: 0.8740 (t) cc_final: 0.8309 (p) REVERT: A 565 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7924 (ttt90) REVERT: A 783 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7223 (pttp) REVERT: A 829 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8078 (mmtm) REVERT: A 892 GLU cc_start: 0.6608 (tm-30) cc_final: 0.6192 (pp20) REVERT: A 1137 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7368 (ttp-170) REVERT: B 294 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7877 (mtp-110) REVERT: B 565 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7024 (ttp-170) REVERT: B 841 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8311 (tptp) REVERT: B 892 GLU cc_start: 0.6269 (tm-30) cc_final: 0.5874 (pp20) REVERT: B 1158 LYS cc_start: 0.7963 (mtmp) cc_final: 0.7699 (mtmm) REVERT: C 133 ARG cc_start: 0.7833 (tmm-80) cc_final: 0.7567 (tmm160) REVERT: C 170 VAL cc_start: 0.8424 (p) cc_final: 0.7973 (m) REVERT: C 180 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: C 190 GLU cc_start: 0.7424 (mp0) cc_final: 0.7019 (mp0) REVERT: C 252 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6268 (mmt) REVERT: C 346 PHE cc_start: 0.7382 (m-10) cc_final: 0.7129 (m-10) REVERT: C 348 GLU cc_start: 0.7759 (tp30) cc_final: 0.7429 (tp30) REVERT: C 354 MET cc_start: 0.7396 (mtp) cc_final: 0.7181 (mtt) REVERT: C 565 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7758 (ttt90) REVERT: C 788 ASN cc_start: 0.7813 (p0) cc_final: 0.7576 (p0) REVERT: C 829 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8121 (mmpt) REVERT: C 876 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7615 (m-80) REVERT: D 128 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8022 (tt) REVERT: D 180 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7883 (tp40) REVERT: D 192 MET cc_start: 0.5742 (mtp) cc_final: 0.5401 (mpp) REVERT: D 252 MET cc_start: 0.6704 (tpt) cc_final: 0.6397 (mpt) REVERT: D 308 CYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7930 (m) REVERT: D 354 MET cc_start: 0.7297 (mtp) cc_final: 0.7045 (mtt) REVERT: D 426 SER cc_start: 0.8666 (t) cc_final: 0.8271 (p) REVERT: D 565 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7005 (ttp-170) REVERT: D 786 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8178 (mppt) REVERT: D 892 GLU cc_start: 0.6390 (tm-30) cc_final: 0.6018 (pp20) outliers start: 72 outliers final: 49 residues processed: 580 average time/residue: 1.3636 time to fit residues: 927.7077 Evaluate side-chains 586 residues out of total 3236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 523 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 565 ARG Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 565 ARG Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 841 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 959 MET Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 831 LEU Chi-restraints excluded: chain C residue 876 TYR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 308 CYS Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 565 ARG Chi-restraints excluded: chain D residue 602 ASP Chi-restraints excluded: chain D residue 805 VAL Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 959 MET Chi-restraints excluded: chain D residue 969 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 1.9990 chunk 300 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 260 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 52 optimal weight: 9.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 845 HIS B 180 GLN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 HIS ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 632 ASN C 845 HIS D 156 ASN D 251 ASN D 845 HIS D 931 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.125905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092506 restraints weight = 49967.218| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.07 r_work: 0.3097 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 29344 Z= 0.466 Angle : 0.716 14.460 39812 Z= 0.343 Chirality : 0.048 0.305 4548 Planarity : 0.006 0.126 4992 Dihedral : 4.850 39.807 3909 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 2.70 % Allowed : 24.02 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3532 helix: 1.21 (0.12), residues: 1728 sheet: -0.26 (0.29), residues: 344 loop : 0.01 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 177 HIS 0.008 0.002 HIS C1046 PHE 0.028 0.002 PHE B 283 TYR 0.019 0.002 TYR C 403 ARG 0.015 0.001 ARG A 948 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13536.44 seconds wall clock time: 238 minutes 25.86 seconds (14305.86 seconds total)