Starting phenix.real_space_refine on Thu Feb 15 07:39:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/02_2024/7oh7_12896_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.023 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 P 5 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7455 2.51 5 N 1863 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A ARG 1117": "NH1" <-> "NH2" Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 359": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11552 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2842 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {' MG': 1, '2Y5': 1, 'ACP': 1} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} Time building chain proxies: 6.68, per 1000 atoms: 0.58 Number of scatterers: 11552 At special positions: 0 Unit cell: (79.4024, 105.182, 171.179, 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) S 48 16.00 P 5 15.00 Mg 1 11.99 O 2180 8.00 N 1863 7.00 C 7455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.3 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 11 sheets defined 38.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 214 through 221 removed outlier: 4.211A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.976A pdb=" N GLN A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.700A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 439 through 472 Processing helix chain 'A' and resid 488 through 505 removed outlier: 3.533A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASN A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 525 removed outlier: 4.758A pdb=" N VAL A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 619 through 632 removed outlier: 3.754A pdb=" N ASN A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 628 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 630 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 632 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.868A pdb=" N LEU A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG A 730 " --> pdb=" O VAL A 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 730' Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 766 through 781 Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.689A pdb=" N HIS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.612A pdb=" N ASN A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 891' Processing helix chain 'A' and resid 899 through 904 Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 931 through 943 removed outlier: 4.691A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.795A pdb=" N VAL A 959 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N SER A 960 " --> pdb=" O ASN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 996 removed outlier: 3.582A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1020 removed outlier: 4.263A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A1009 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1031 removed outlier: 4.281A pdb=" N VAL A1030 " --> pdb=" O GLN A1026 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE A1031 " --> pdb=" O PHE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1050 removed outlier: 4.197A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1077 through 1085 removed outlier: 4.072A pdb=" N LYS A1085 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1115 removed outlier: 3.622A pdb=" N ILE A1115 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1153 removed outlier: 3.741A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1186 removed outlier: 3.563A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Proline residue: A1177 - end of helix Proline residue: A1184 - end of helix Processing helix chain 'A' and resid 1195 through 1199 Processing helix chain 'A' and resid 1205 through 1229 removed outlier: 4.017A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 5.030A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 46 through 68 Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 331 through 356 removed outlier: 3.627A pdb=" N ILE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.534A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 307 through 310 removed outlier: 7.114A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.858A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 383 through 387 removed outlier: 3.869A pdb=" N GLY A 384 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.841A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS A 830 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER A 559 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP A 832 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= H, first strand: chain 'A' and resid 687 through 690 removed outlier: 3.541A pdb=" N SER A 676 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 673 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 678 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE A 671 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 680 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE A 669 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 570 through 577 removed outlier: 6.928A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.771A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 110 through 115 removed outlier: 4.408A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1113 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: 4.23 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1865 1.32 - 1.45: 3461 1.45 - 1.59: 6402 1.59 - 1.73: 7 1.73 - 1.86: 79 Bond restraints: 11814 Sorted by residual: bond pdb=" C1' ACP A1502 " pdb=" O4' ACP A1502 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ACP A1502 " pdb=" C2' ACP A1502 " ideal model delta sigma weight residual 1.527 1.309 0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C4' ACP A1502 " pdb=" O4' ACP A1502 " ideal model delta sigma weight residual 1.428 1.302 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C6 ACP A1502 " pdb=" N6 ACP A1502 " ideal model delta sigma weight residual 1.335 1.452 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C2' ACP A1502 " pdb=" O2' ACP A1502 " ideal model delta sigma weight residual 1.401 1.494 -0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 11809 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.49: 398 107.49 - 114.50: 7050 114.50 - 121.51: 5879 121.51 - 128.53: 2607 128.53 - 135.54: 89 Bond angle restraints: 16023 Sorted by residual: angle pdb=" C21 2Y5 A1501 " pdb=" C22 2Y5 A1501 " pdb=" C23 2Y5 A1501 " ideal model delta sigma weight residual 85.82 120.65 -34.83 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " ideal model delta sigma weight residual 152.70 119.58 33.12 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C18 2Y5 A1501 " pdb=" C19 2Y5 A1501 " pdb=" C20 2Y5 A1501 " ideal model delta sigma weight residual 152.65 120.32 32.33 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C15 2Y5 A1501 " pdb=" C16 2Y5 A1501 " pdb=" C17 2Y5 A1501 " ideal model delta sigma weight residual 152.62 120.81 31.81 3.00e+00 1.11e-01 1.12e+02 angle pdb=" O3A ACP A1502 " pdb=" PA ACP A1502 " pdb=" O5' ACP A1502 " ideal model delta sigma weight residual 93.75 109.63 -15.88 3.00e+00 1.11e-01 2.80e+01 ... (remaining 16018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 7034 35.64 - 71.27: 92 71.27 - 106.91: 25 106.91 - 142.55: 4 142.55 - 178.19: 2 Dihedral angle restraints: 7157 sinusoidal: 3007 harmonic: 4150 Sorted by residual: dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N ILE A 671 " pdb=" CA ILE A 671 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " pdb=" C27 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual -30.76 147.43 -178.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 2Y5 A1501 " pdb=" O1 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O13 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 64.28 -132.91 -162.81 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 7154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1693 0.075 - 0.149: 138 0.149 - 0.224: 0 0.224 - 0.298: 2 0.298 - 0.373: 1 Chirality restraints: 1834 Sorted by residual: chirality pdb=" C2' ACP A1502 " pdb=" C1' ACP A1502 " pdb=" C3' ACP A1502 " pdb=" O2' ACP A1502 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C5 BMA E 4 " pdb=" C4 BMA E 4 " pdb=" C6 BMA E 4 " pdb=" O5 BMA E 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1831 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 621 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C PRO A 621 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO A 621 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 622 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 745 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C HIS A 745 " 0.059 2.00e-02 2.50e+03 pdb=" O HIS A 745 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 746 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 746 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C LEU A 746 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 746 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU A 747 " 0.017 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 168 2.65 - 3.21: 10723 3.21 - 3.77: 17283 3.77 - 4.34: 24092 4.34 - 4.90: 39112 Nonbonded interactions: 91378 Sorted by model distance: nonbonded pdb=" OD1 ASP A 954 " pdb="MG MG A1503 " model vdw 2.086 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1503 " model vdw 2.088 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1601 " model vdw 2.089 2.170 nonbonded pdb=" OD2 ASP A 560 " pdb="MG MG A1503 " model vdw 2.089 2.170 nonbonded pdb="MG MG A1503 " pdb=" O HOH A1603 " model vdw 2.102 2.170 ... (remaining 91373 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 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.130 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 35.690 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 11814 Z= 0.342 Angle : 0.825 34.828 16023 Z= 0.362 Chirality : 0.042 0.373 1834 Planarity : 0.005 0.064 1995 Dihedral : 13.843 178.186 4475 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.20 % Allowed : 5.51 % Favored : 93.30 % 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: -3.01 (0.20), residues: 1410 helix: -1.63 (0.19), residues: 571 sheet: -2.02 (0.31), residues: 218 loop : -2.23 (0.22), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1132 HIS 0.003 0.000 HIS A 745 PHE 0.009 0.001 PHE A1205 TYR 0.013 0.001 TYR C 140 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 277 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ASP cc_start: 0.7367 (t70) cc_final: 0.6549 (t0) REVERT: A 386 MET cc_start: 0.6339 (ttm) cc_final: 0.6114 (tmm) REVERT: A 528 ASP cc_start: 0.6644 (t0) cc_final: 0.6361 (t0) REVERT: A 565 LEU cc_start: 0.8193 (mt) cc_final: 0.7956 (mt) REVERT: A 585 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8206 (tptp) REVERT: A 648 TYR cc_start: 0.7613 (m-80) cc_final: 0.7244 (m-10) REVERT: A 649 GLN cc_start: 0.8409 (mt0) cc_final: 0.7873 (mt0) REVERT: A 672 ARG cc_start: 0.8360 (ttt180) cc_final: 0.7641 (tpt170) REVERT: A 948 LEU cc_start: 0.5891 (mt) cc_final: 0.5321 (mt) REVERT: C 74 THR cc_start: 0.6374 (m) cc_final: 0.6153 (p) REVERT: C 297 LYS cc_start: 0.7509 (mttt) cc_final: 0.7062 (tttt) outliers start: 15 outliers final: 4 residues processed: 289 average time/residue: 0.2869 time to fit residues: 111.3524 Evaluate side-chains 154 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 0.0070 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN A 891 ASN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 HIS C 246 ASN ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11814 Z= 0.178 Angle : 0.599 12.954 16023 Z= 0.298 Chirality : 0.044 0.228 1834 Planarity : 0.004 0.051 1995 Dihedral : 13.591 174.899 1770 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.55 % Allowed : 11.65 % Favored : 85.79 % 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: -2.08 (0.21), residues: 1410 helix: -0.82 (0.21), residues: 579 sheet: -1.39 (0.32), residues: 220 loop : -1.83 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 299 HIS 0.008 0.001 HIS A 745 PHE 0.020 0.001 PHE A 605 TYR 0.023 0.001 TYR C 77 ARG 0.006 0.000 ARG C 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.6373 (t80) REVERT: A 585 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8125 (tptp) REVERT: A 624 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8341 (p0) REVERT: A 672 ARG cc_start: 0.8417 (ttt180) cc_final: 0.7665 (tpt170) REVERT: A 1041 MET cc_start: 0.5868 (mtt) cc_final: 0.5661 (mtt) REVERT: C 273 MET cc_start: 0.7928 (mmp) cc_final: 0.7726 (mmm) REVERT: C 297 LYS cc_start: 0.7604 (mttt) cc_final: 0.7026 (tttt) outliers start: 32 outliers final: 21 residues processed: 172 average time/residue: 0.2480 time to fit residues: 61.0306 Evaluate side-chains 163 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 853 SER Chi-restraints excluded: chain A residue 891 ASN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 891 ASN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11814 Z= 0.153 Angle : 0.564 12.453 16023 Z= 0.278 Chirality : 0.042 0.159 1834 Planarity : 0.004 0.035 1995 Dihedral : 12.073 168.507 1770 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.23 % Allowed : 13.09 % Favored : 84.68 % 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: -1.69 (0.21), residues: 1410 helix: -0.48 (0.22), residues: 584 sheet: -1.21 (0.32), residues: 227 loop : -1.64 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.005 0.001 HIS A 883 PHE 0.020 0.001 PHE A1175 TYR 0.018 0.001 TYR C 77 ARG 0.003 0.000 ARG A 943 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6379 (t80) REVERT: A 570 MET cc_start: 0.6293 (mmt) cc_final: 0.5830 (mmm) REVERT: A 585 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8135 (tptp) REVERT: A 624 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8367 (p0) REVERT: A 672 ARG cc_start: 0.8407 (ttt180) cc_final: 0.7623 (tpt170) REVERT: A 743 MET cc_start: 0.8452 (mmm) cc_final: 0.8243 (mmp) REVERT: A 1085 LYS cc_start: 0.7776 (mttt) cc_final: 0.7361 (mmtt) REVERT: A 1124 MET cc_start: 0.6857 (ptp) cc_final: 0.6637 (ptp) REVERT: C 64 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7554 (pp) REVERT: C 297 LYS cc_start: 0.7605 (mttt) cc_final: 0.7030 (tttt) REVERT: C 330 MET cc_start: 0.6855 (mmm) cc_final: 0.6466 (mmm) outliers start: 28 outliers final: 20 residues processed: 161 average time/residue: 0.2389 time to fit residues: 55.8831 Evaluate side-chains 153 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 61 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11814 Z= 0.219 Angle : 0.593 12.396 16023 Z= 0.293 Chirality : 0.043 0.153 1834 Planarity : 0.004 0.038 1995 Dihedral : 10.864 169.334 1770 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.27 % Allowed : 13.17 % Favored : 83.56 % 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: -1.42 (0.22), residues: 1410 helix: -0.28 (0.22), residues: 578 sheet: -0.94 (0.33), residues: 226 loop : -1.51 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1044 HIS 0.005 0.001 HIS C 79 PHE 0.024 0.002 PHE A1175 TYR 0.018 0.001 TYR A1116 ARG 0.002 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 126 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6499 (t80) REVERT: A 570 MET cc_start: 0.6578 (mmt) cc_final: 0.6151 (mmm) REVERT: A 585 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8140 (tptp) REVERT: A 624 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8401 (p0) REVERT: A 672 ARG cc_start: 0.8388 (ttt180) cc_final: 0.7645 (tpt170) REVERT: A 1085 LYS cc_start: 0.7852 (mttt) cc_final: 0.7430 (mmtt) REVERT: A 1124 MET cc_start: 0.7154 (ptp) cc_final: 0.6863 (ptp) REVERT: C 297 LYS cc_start: 0.7624 (mttt) cc_final: 0.7135 (tttt) outliers start: 41 outliers final: 31 residues processed: 156 average time/residue: 0.2436 time to fit residues: 55.7962 Evaluate side-chains 154 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11814 Z= 0.228 Angle : 0.615 12.499 16023 Z= 0.301 Chirality : 0.043 0.147 1834 Planarity : 0.003 0.038 1995 Dihedral : 10.474 169.810 1770 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.43 % Allowed : 13.73 % Favored : 82.84 % 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: -1.39 (0.22), residues: 1410 helix: -0.35 (0.22), residues: 588 sheet: -0.82 (0.33), residues: 224 loop : -1.42 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1044 HIS 0.004 0.001 HIS A 634 PHE 0.026 0.002 PHE A1175 TYR 0.017 0.001 TYR C 140 ARG 0.004 0.000 ARG A 943 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6524 (t80) REVERT: A 570 MET cc_start: 0.6589 (mmt) cc_final: 0.6167 (mmm) REVERT: A 640 PHE cc_start: 0.7336 (m-10) cc_final: 0.6067 (t80) REVERT: A 784 ASP cc_start: 0.8117 (t0) cc_final: 0.7788 (t70) REVERT: A 1085 LYS cc_start: 0.7876 (mttt) cc_final: 0.7420 (mmtt) REVERT: A 1124 MET cc_start: 0.7223 (ptp) cc_final: 0.6939 (ptp) REVERT: C 297 LYS cc_start: 0.7582 (mttt) cc_final: 0.7058 (tttt) outliers start: 43 outliers final: 34 residues processed: 160 average time/residue: 0.2234 time to fit residues: 53.1448 Evaluate side-chains 152 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 862 ASN Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.4980 chunk 122 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.0670 chunk 11 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11814 Z= 0.147 Angle : 0.577 12.436 16023 Z= 0.280 Chirality : 0.042 0.147 1834 Planarity : 0.003 0.039 1995 Dihedral : 10.097 170.553 1770 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.63 % Allowed : 15.08 % Favored : 82.28 % 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: -1.12 (0.22), residues: 1410 helix: -0.11 (0.22), residues: 578 sheet: -0.73 (0.33), residues: 224 loop : -1.28 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 772 HIS 0.005 0.001 HIS A 634 PHE 0.020 0.001 PHE A 572 TYR 0.017 0.001 TYR C 140 ARG 0.003 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7525 (pp30) REVERT: A 533 TYR cc_start: 0.6862 (OUTLIER) cc_final: 0.6431 (t80) REVERT: A 570 MET cc_start: 0.6325 (mmt) cc_final: 0.5954 (mmm) REVERT: A 640 PHE cc_start: 0.7426 (m-10) cc_final: 0.6008 (t80) REVERT: A 952 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7329 (pt) REVERT: A 1085 LYS cc_start: 0.7902 (mttt) cc_final: 0.7449 (mmtt) REVERT: A 1124 MET cc_start: 0.7080 (ptp) cc_final: 0.6837 (ptp) REVERT: C 297 LYS cc_start: 0.7542 (mttt) cc_final: 0.6967 (tttt) REVERT: C 300 MET cc_start: 0.8333 (tpp) cc_final: 0.8086 (tpt) outliers start: 33 outliers final: 25 residues processed: 148 average time/residue: 0.2285 time to fit residues: 50.9190 Evaluate side-chains 147 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11814 Z= 0.150 Angle : 0.583 12.412 16023 Z= 0.282 Chirality : 0.042 0.160 1834 Planarity : 0.003 0.039 1995 Dihedral : 9.888 171.637 1770 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.63 % Allowed : 16.20 % Favored : 81.17 % 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: -0.99 (0.22), residues: 1410 helix: -0.01 (0.22), residues: 577 sheet: -0.63 (0.33), residues: 224 loop : -1.20 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 772 HIS 0.004 0.001 HIS A 634 PHE 0.028 0.001 PHE A1175 TYR 0.016 0.001 TYR C 140 ARG 0.003 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7790 (pp30) REVERT: A 533 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 570 MET cc_start: 0.6329 (mmt) cc_final: 0.5971 (mmm) REVERT: A 640 PHE cc_start: 0.7324 (m-10) cc_final: 0.6110 (t80) REVERT: A 648 TYR cc_start: 0.8427 (m-10) cc_final: 0.8118 (m-10) REVERT: A 952 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7317 (pt) REVERT: A 1085 LYS cc_start: 0.7907 (mttt) cc_final: 0.7464 (mmtt) REVERT: A 1124 MET cc_start: 0.7135 (ptp) cc_final: 0.6927 (ptp) REVERT: C 297 LYS cc_start: 0.7527 (mttt) cc_final: 0.6938 (tttt) REVERT: C 300 MET cc_start: 0.8315 (tpp) cc_final: 0.8019 (tpt) outliers start: 33 outliers final: 26 residues processed: 145 average time/residue: 0.2269 time to fit residues: 49.3982 Evaluate side-chains 147 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 67 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11814 Z= 0.137 Angle : 0.575 12.800 16023 Z= 0.277 Chirality : 0.042 0.218 1834 Planarity : 0.003 0.040 1995 Dihedral : 9.714 172.918 1770 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.31 % Allowed : 16.36 % Favored : 81.32 % 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: -0.92 (0.22), residues: 1410 helix: 0.04 (0.22), residues: 582 sheet: -0.59 (0.33), residues: 226 loop : -1.16 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.003 0.001 HIS A 883 PHE 0.029 0.001 PHE A1175 TYR 0.015 0.001 TYR C 140 ARG 0.003 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6468 (t80) REVERT: A 570 MET cc_start: 0.6319 (mmt) cc_final: 0.5929 (mmm) REVERT: A 640 PHE cc_start: 0.7336 (m-10) cc_final: 0.6098 (t80) REVERT: A 648 TYR cc_start: 0.8429 (m-10) cc_final: 0.8142 (m-10) REVERT: A 761 MET cc_start: 0.4686 (ttt) cc_final: 0.4464 (ttp) REVERT: A 1085 LYS cc_start: 0.7926 (mttt) cc_final: 0.7412 (mmtt) REVERT: C 273 MET cc_start: 0.7595 (mmp) cc_final: 0.7370 (mmm) REVERT: C 297 LYS cc_start: 0.7495 (mttt) cc_final: 0.6935 (tttt) REVERT: C 300 MET cc_start: 0.8301 (tpp) cc_final: 0.7972 (tpt) outliers start: 29 outliers final: 25 residues processed: 149 average time/residue: 0.2410 time to fit residues: 52.5543 Evaluate side-chains 146 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 130 optimal weight: 0.0270 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 114 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11814 Z= 0.154 Angle : 0.588 12.948 16023 Z= 0.283 Chirality : 0.042 0.167 1834 Planarity : 0.003 0.040 1995 Dihedral : 9.590 175.255 1770 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.39 % Allowed : 16.36 % Favored : 81.25 % 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: -0.80 (0.22), residues: 1410 helix: 0.08 (0.22), residues: 582 sheet: -0.34 (0.34), residues: 212 loop : -1.12 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1134 HIS 0.004 0.001 HIS A 634 PHE 0.030 0.001 PHE A1175 TYR 0.015 0.001 TYR C 140 ARG 0.004 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.1236 (ptm) cc_final: 0.0558 (mpp) REVERT: A 533 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6532 (t80) REVERT: A 570 MET cc_start: 0.6359 (mmt) cc_final: 0.5950 (mmm) REVERT: A 640 PHE cc_start: 0.7358 (m-10) cc_final: 0.6148 (t80) REVERT: A 648 TYR cc_start: 0.8519 (m-10) cc_final: 0.8221 (m-10) REVERT: A 1085 LYS cc_start: 0.7951 (mttt) cc_final: 0.7434 (mmtt) REVERT: C 273 MET cc_start: 0.7504 (mmp) cc_final: 0.7276 (mmm) REVERT: C 297 LYS cc_start: 0.7488 (mttt) cc_final: 0.6950 (tttt) outliers start: 30 outliers final: 27 residues processed: 147 average time/residue: 0.2405 time to fit residues: 52.1862 Evaluate side-chains 147 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.0040 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11814 Z= 0.242 Angle : 0.673 21.453 16023 Z= 0.324 Chirality : 0.044 0.151 1834 Planarity : 0.004 0.042 1995 Dihedral : 9.740 178.639 1770 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.63 % Allowed : 16.12 % Favored : 81.25 % 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: -0.88 (0.22), residues: 1410 helix: -0.03 (0.22), residues: 578 sheet: -0.45 (0.34), residues: 212 loop : -1.06 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1044 HIS 0.004 0.001 HIS C 79 PHE 0.032 0.002 PHE A1175 TYR 0.015 0.001 TYR C 140 ARG 0.008 0.000 ARG A 943 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.1275 (ptm) cc_final: 0.0696 (mpp) REVERT: A 520 TYR cc_start: 0.6688 (m-10) cc_final: 0.6465 (m-10) REVERT: A 533 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.6465 (t80) REVERT: A 570 MET cc_start: 0.6511 (mmt) cc_final: 0.6179 (mmm) REVERT: A 640 PHE cc_start: 0.7385 (m-10) cc_final: 0.6216 (t80) REVERT: A 648 TYR cc_start: 0.8538 (m-10) cc_final: 0.8276 (m-10) REVERT: A 1085 LYS cc_start: 0.8050 (mttt) cc_final: 0.7454 (mmtt) REVERT: A 1107 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 1124 MET cc_start: 0.6673 (ptp) cc_final: 0.6435 (pmm) REVERT: C 185 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7307 (mmtt) REVERT: C 297 LYS cc_start: 0.7585 (mttt) cc_final: 0.7015 (tttt) outliers start: 33 outliers final: 28 residues processed: 142 average time/residue: 0.2309 time to fit residues: 48.5543 Evaluate side-chains 147 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 333 TYR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 179 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 98 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.140061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104263 restraints weight = 28726.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.104799 restraints weight = 18575.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105653 restraints weight = 12872.004| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11814 Z= 0.209 Angle : 0.644 17.643 16023 Z= 0.310 Chirality : 0.043 0.160 1834 Planarity : 0.003 0.041 1995 Dihedral : 9.490 175.629 1770 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.39 % Allowed : 16.84 % Favored : 80.77 % 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: -0.82 (0.22), residues: 1410 helix: 0.04 (0.22), residues: 577 sheet: -0.47 (0.34), residues: 212 loop : -1.04 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1044 HIS 0.003 0.001 HIS A 634 PHE 0.031 0.002 PHE A1175 TYR 0.021 0.001 TYR C 140 ARG 0.004 0.000 ARG A 943 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2362.10 seconds wall clock time: 44 minutes 4.99 seconds (2644.99 seconds total)