Starting phenix.real_space_refine (version: dev) on Tue Apr 5 06:50:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_12896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_12896.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_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_12896/04_2022/7oh7_12896_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_12896_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_12896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_12896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_12896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh7_12896/04_2022/7oh7_12896_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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 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 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: 2 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 100 Unusual residues: {'ACP': 1, '2Y5': 1, ' MG': 1} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} Time building chain proxies: 7.15, per 1000 atoms: 0.62 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: 5.56 Conformation dependent library (CDL) restraints added in 1.8 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: 2.33 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: 4.17 Time building geometry restraints manager: 5.58 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=" C15 2Y5 A1501 " pdb=" C16 2Y5 A1501 " pdb=" C17 2Y5 A1501 " ideal model delta sigma weight residual 85.84 120.81 -34.97 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " ideal model delta sigma weight residual 152.66 119.58 33.08 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 152.68 120.32 32.36 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C21 2Y5 A1501 " pdb=" C22 2Y5 A1501 " pdb=" C23 2Y5 A1501 " ideal model delta sigma weight residual 152.64 120.65 31.99 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C22 2Y5 A1501 " pdb=" C23 2Y5 A1501 " pdb=" C24 2Y5 A1501 " ideal model delta sigma weight residual 131.57 108.96 22.61 3.00e+00 1.11e-01 5.68e+01 ... (remaining 16018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.84: 6858 27.84 - 55.67: 139 55.67 - 83.51: 11 83.51 - 111.34: 3 111.34 - 139.18: 2 Dihedral angle restraints: 7013 sinusoidal: 2863 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=" C16 2Y5 A1501 " pdb=" C17 2Y5 A1501 " pdb=" C18 2Y5 A1501 " pdb=" C19 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 69.21 -151.61 -139.18 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" CA ILE A 187 " pdb=" C ILE A 187 " pdb=" N ASN A 188 " pdb=" CA ASN A 188 " ideal model delta harmonic sigma weight residual 180.00 -159.90 -20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 7010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1703 0.075 - 0.149: 130 0.149 - 0.224: 0 0.224 - 0.298: 0 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=" CA ILE A 322 " pdb=" N ILE A 322 " pdb=" C ILE A 322 " pdb=" CB ILE A 322 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE C 129 " pdb=" N ILE C 129 " pdb=" C ILE C 129 " pdb=" CB ILE C 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (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 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. 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: 1.020 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: 0.010 Extract box with map and model: 4.540 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.100 Process input model: 34.100 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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= 0.332 Angle : 0.825 34.966 16023 Z= 0.363 Chirality : 0.040 0.373 1834 Planarity : 0.005 0.064 1995 Dihedral : 11.308 139.177 4331 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.20 % 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 *********************** 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 : 1.221 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 outliers start: 15 outliers final: 4 residues processed: 289 average time/residue: 0.2740 time to fit residues: 107.2371 Evaluate side-chains 150 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1080 time to fit residues: 2.7406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 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: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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: 0.7104 moved from start: 0.2307 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= 0.204 Angle : 0.618 12.699 16023 Z= 0.310 Chirality : 0.044 0.238 1834 Planarity : 0.004 0.055 1995 Dihedral : 8.717 127.325 1619 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 2.95 % 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: -2.09 (0.21), residues: 1410 helix: -0.83 (0.21), residues: 583 sheet: -1.35 (0.32), residues: 220 loop : -1.86 (0.24), residues: 607 *********************** 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 182 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.330 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 outliers start: 37 outliers final: 25 residues processed: 171 average time/residue: 0.2422 time to fit residues: 59.6061 Evaluate side-chains 155 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1298 time to fit residues: 7.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 0.0470 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 0.0020 chunk 128 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 overall best weight: 0.5888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN ** A 862 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7080 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 11814 Z= 0.157 Angle : 0.567 11.892 16023 Z= 0.282 Chirality : 0.042 0.158 1834 Planarity : 0.004 0.034 1995 Dihedral : 8.414 127.023 1619 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 0.88 % 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: -1.71 (0.22), residues: 1410 helix: -0.49 (0.21), residues: 591 sheet: -1.10 (0.33), residues: 222 loop : -1.72 (0.24), residues: 597 *********************** 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 159 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 1.408 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 outliers start: 11 outliers final: 5 residues processed: 157 average time/residue: 0.2350 time to fit residues: 54.6222 Evaluate side-chains 126 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1091 time to fit residues: 2.9898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 825 GLN C 364 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 11814 Z= 0.396 Angle : 0.766 11.709 16023 Z= 0.390 Chirality : 0.049 0.197 1834 Planarity : 0.005 0.038 1995 Dihedral : 8.536 121.736 1619 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 2.79 % 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: -1.98 (0.21), residues: 1410 helix: -0.81 (0.21), residues: 588 sheet: -0.98 (0.34), residues: 213 loop : -1.86 (0.24), residues: 609 *********************** 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 155 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 145 average time/residue: 0.2257 time to fit residues: 48.8814 Evaluate side-chains 127 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.433 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1129 time to fit residues: 6.4744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 1 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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** A 989 GLN ** 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: 0.7281 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 11814 Z= 0.242 Angle : 0.639 11.578 16023 Z= 0.320 Chirality : 0.044 0.165 1834 Planarity : 0.004 0.080 1995 Dihedral : 8.267 124.152 1619 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.64 % 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: -1.61 (0.22), residues: 1410 helix: -0.46 (0.22), residues: 581 sheet: -0.89 (0.34), residues: 211 loop : -1.63 (0.24), residues: 618 *********************** 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 129 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 129 average time/residue: 0.2205 time to fit residues: 42.6261 Evaluate side-chains 112 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1036 time to fit residues: 2.5841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.0050 chunk 11 optimal weight: 0.0980 chunk 71 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** 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: 0.7222 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 11814 Z= 0.161 Angle : 0.590 11.664 16023 Z= 0.293 Chirality : 0.042 0.153 1834 Planarity : 0.003 0.046 1995 Dihedral : 7.946 122.517 1619 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.96 % 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 (0.22), residues: 1410 helix: -0.19 (0.22), residues: 585 sheet: -0.58 (0.34), residues: 206 loop : -1.42 (0.25), residues: 619 *********************** 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 131 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.2234 time to fit residues: 42.9883 Evaluate side-chains 121 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.404 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1178 time to fit residues: 3.6767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 31 GLN ** 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: 0.7256 moved from start: 0.3892 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= 0.203 Angle : 0.604 11.929 16023 Z= 0.300 Chirality : 0.043 0.150 1834 Planarity : 0.003 0.043 1995 Dihedral : 7.765 119.117 1619 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.96 % 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: -1.14 (0.22), residues: 1410 helix: -0.15 (0.22), residues: 586 sheet: -0.66 (0.34), residues: 211 loop : -1.29 (0.25), residues: 613 *********************** 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 127 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 0.2282 time to fit residues: 42.4145 Evaluate side-chains 121 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1127 time to fit residues: 3.3659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.0770 chunk 40 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8100 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 11814 Z= 0.158 Angle : 0.590 12.398 16023 Z= 0.289 Chirality : 0.042 0.151 1834 Planarity : 0.003 0.045 1995 Dihedral : 7.593 117.021 1619 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.56 % 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: -0.89 (0.23), residues: 1410 helix: 0.05 (0.22), residues: 580 sheet: -0.63 (0.33), residues: 213 loop : -1.10 (0.26), residues: 617 *********************** 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 128 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 125 average time/residue: 0.2339 time to fit residues: 44.0034 Evaluate side-chains 115 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1294 time to fit residues: 2.3029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 7.9990 chunk 130 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 0.0270 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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** A 839 GLN ** 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: 0.7186 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 11814 Z= 0.153 Angle : 0.587 12.740 16023 Z= 0.290 Chirality : 0.042 0.153 1834 Planarity : 0.003 0.046 1995 Dihedral : 7.424 113.603 1619 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.72 % 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: -0.75 (0.23), residues: 1410 helix: 0.27 (0.23), residues: 569 sheet: -0.61 (0.33), residues: 212 loop : -1.08 (0.25), residues: 629 *********************** 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 127 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 125 average time/residue: 0.2276 time to fit residues: 42.2801 Evaluate side-chains 119 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1554 time to fit residues: 3.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.0010 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 0.1980 chunk 129 optimal weight: 0.3980 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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** ** A 839 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: 0.7180 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 11814 Z= 0.156 Angle : 0.636 22.812 16023 Z= 0.302 Chirality : 0.042 0.157 1834 Planarity : 0.003 0.047 1995 Dihedral : 7.288 110.365 1619 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.24 % 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: -0.68 (0.23), residues: 1410 helix: 0.33 (0.23), residues: 571 sheet: -0.71 (0.33), residues: 219 loop : -1.00 (0.26), residues: 620 ********************** 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 118 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 0.2304 time to fit residues: 39.9359 Evaluate side-chains 114 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1560 time to fit residues: 2.0853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 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 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.106523 restraints weight = 28767.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106262 restraints weight = 19343.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.107025 restraints weight = 14075.702| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4175 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= 0.161 Angle : 0.615 18.341 16023 Z= 0.296 Chirality : 0.042 0.158 1834 Planarity : 0.003 0.047 1995 Dihedral : 7.159 106.279 1619 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.08 % 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: -0.64 (0.23), residues: 1410 helix: 0.34 (0.23), residues: 571 sheet: -0.66 (0.33), residues: 219 loop : -0.97 (0.26), residues: 620 =============================================================================== Job complete usr+sys time: 2117.77 seconds wall clock time: 39 minutes 47.24 seconds (2387.24 seconds total)