Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 19:28:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfw_30666/04_2023/7dfw_30666_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfw_30666/04_2023/7dfw_30666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfw_30666/04_2023/7dfw_30666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfw_30666/04_2023/7dfw_30666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfw_30666/04_2023/7dfw_30666_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfw_30666/04_2023/7dfw_30666_neut_trim_updated.pdb" } resolution = 2.69 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= 0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 46 5.16 5 C 5195 2.51 5 N 1226 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 391": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 545": "OD1" <-> "OD2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 726": "NH1" <-> "NH2" Residue "A ARG 727": "NH1" <-> "NH2" Residue "A ARG 738": "NH1" <-> "NH2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A ARG 801": "NH1" <-> "NH2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A PHE 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1187": "NH1" <-> "NH2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A ARG 1279": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7913 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7450 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 50, 'TRANS': 906} Chain: "I" 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: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 351 Unusual residues: {'CLR': 6, 'LMT': 1, 'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 14} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.00, per 1000 atoms: 0.63 Number of scatterers: 7913 At special positions: 0 Unit cell: (98.19, 75.279, 135.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 1445 8.00 N 1226 7.00 C 5195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " 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 " NAG S 2 " - " NAG S 3 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " NAG L 3 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 431 " " NAG A1302 " - " ASN A 464 " " NAG A1303 " - " ASN A 506 " " NAG A1304 " - " ASN A 416 " " NAG A1305 " - " ASN A 479 " " NAG A1306 " - " ASN A 927 " " NAG A1307 " - " ASN A1075 " " NAG I 1 " - " ASN A 497 " " NAG L 1 " - " ASN A 909 " " NAG S 1 " - " ASN A1037 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 5 sheets defined 54.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 352 through 369 Proline residue: A 362 - end of helix removed outlier: 4.379A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 389 through 401 Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 467 through 470 No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 491 through 494 Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 518 through 527 removed outlier: 3.857A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 585 through 606 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 630 through 646 Proline residue: A 634 - end of helix removed outlier: 4.110A pdb=" N THR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 666 through 689 Processing helix chain 'A' and resid 696 through 723 Proline residue: A 703 - end of helix removed outlier: 3.584A pdb=" N LEU A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASP A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 763 removed outlier: 3.660A pdb=" N ARG A 742 " --> pdb=" O ARG A 738 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.720A pdb=" N SER A 751 " --> pdb=" O MET A 747 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 798 removed outlier: 3.701A pdb=" N PHE A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 803 No H-bonds generated for 'chain 'A' and resid 800 through 803' Processing helix chain 'A' and resid 833 through 840 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.941A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N HIS A 866 " --> pdb=" O TYR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 Processing helix chain 'A' and resid 882 through 893 removed outlier: 3.657A pdb=" N TYR A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 930 through 938 Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 1005 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1059 through 1082 removed outlier: 3.576A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1102 No H-bonds generated for 'chain 'A' and resid 1099 through 1102' Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1108 through 1129 removed outlier: 3.720A pdb=" N VAL A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) Proline residue: A1122 - end of helix removed outlier: 3.729A pdb=" N CYS A1128 " --> pdb=" O PHE A1124 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1158 removed outlier: 3.546A pdb=" N ASN A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A1144 " --> pdb=" O LEU A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1190 removed outlier: 3.708A pdb=" N GLY A1176 " --> pdb=" O VAL A1172 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1229 removed outlier: 4.611A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1217 " --> pdb=" O PHE A1213 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Proline residue: A1222 - end of helix removed outlier: 3.944A pdb=" N LEU A1227 " --> pdb=" O GLY A1223 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A1229 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1241 through 1255 Processing helix chain 'A' and resid 1258 through 1264 removed outlier: 3.626A pdb=" N TYR A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1285 removed outlier: 4.318A pdb=" N GLU A1281 " --> pdb=" O GLN A1277 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A1282 " --> pdb=" O LYS A1278 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 571 through 576 Processing sheet with id= B, first strand: chain 'A' and resid 420 through 423 Processing sheet with id= C, first strand: chain 'A' and resid 505 through 508 Processing sheet with id= D, first strand: chain 'A' and resid 1092 through 1095 removed outlier: 7.023A pdb=" N ASN A1037 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 968 through 970 removed outlier: 3.882A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 948 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: 2.53 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1203 1.31 - 1.44: 2197 1.44 - 1.57: 4640 1.57 - 1.70: 4 1.70 - 1.83: 71 Bond restraints: 8115 Sorted by residual: bond pdb=" C17 P5S A1308 " pdb=" O19 P5S A1308 " ideal model delta sigma weight residual 1.328 1.406 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C38 P5S A1308 " pdb=" O37 P5S A1308 " ideal model delta sigma weight residual 1.331 1.397 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C3' LMT A1309 " pdb=" O3' LMT A1309 " ideal model delta sigma weight residual 1.404 1.350 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C6B LMT A1309 " pdb=" O6B LMT A1309 " ideal model delta sigma weight residual 1.407 1.353 0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C6' LMT A1309 " pdb=" O6' LMT A1309 " ideal model delta sigma weight residual 1.407 1.354 0.053 2.00e-02 2.50e+03 6.98e+00 ... (remaining 8110 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.19: 253 106.19 - 113.24: 4514 113.24 - 120.30: 3171 120.30 - 127.35: 3051 127.35 - 134.41: 86 Bond angle restraints: 11075 Sorted by residual: angle pdb=" O13 P5S A1308 " pdb=" P12 P5S A1308 " pdb=" O15 P5S A1308 " ideal model delta sigma weight residual 120.39 101.73 18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" N ASP A 378 " pdb=" CA ASP A 378 " pdb=" C ASP A 378 " ideal model delta sigma weight residual 109.81 121.79 -11.98 2.21e+00 2.05e-01 2.94e+01 angle pdb=" CA ASP A 378 " pdb=" C ASP A 378 " pdb=" N PRO A 379 " ideal model delta sigma weight residual 118.44 125.35 -6.91 1.59e+00 3.96e-01 1.89e+01 angle pdb=" C LEU A 412 " pdb=" N THR A 413 " pdb=" CA THR A 413 " ideal model delta sigma weight residual 122.78 129.16 -6.38 1.52e+00 4.33e-01 1.76e+01 angle pdb=" CA VAL A 701 " pdb=" C VAL A 701 " pdb=" N VAL A 702 " ideal model delta sigma weight residual 116.60 122.27 -5.67 1.45e+00 4.76e-01 1.53e+01 ... (remaining 11070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.39: 4472 28.39 - 56.77: 133 56.77 - 85.16: 22 85.16 - 113.55: 5 113.55 - 141.93: 2 Dihedral angle restraints: 4634 sinusoidal: 1844 harmonic: 2790 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -173.82 87.82 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A 920 " pdb=" SG CYS A 920 " pdb=" SG CYS A 925 " pdb=" CB CYS A 925 " ideal model delta sinusoidal sigma weight residual -86.00 -18.36 -67.64 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA PRO A1025 " pdb=" C PRO A1025 " pdb=" N LYS A1026 " pdb=" CA LYS A1026 " ideal model delta harmonic sigma weight residual -180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 4631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1081 0.062 - 0.125: 207 0.125 - 0.187: 31 0.187 - 0.249: 15 0.249 - 0.312: 5 Chirality restraints: 1339 Sorted by residual: chirality pdb=" C1 NAG S 3 " pdb=" O3 NAG S 2 " pdb=" C2 NAG S 3 " pdb=" O5 NAG S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" CA ASP A 378 " pdb=" N ASP A 378 " pdb=" C ASP A 378 " pdb=" CB ASP A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB ILE A 996 " pdb=" CA ILE A 996 " pdb=" CG1 ILE A 996 " pdb=" CG2 ILE A 996 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1336 not shown) Planarity restraints: 1343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 3 " -0.346 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG L 3 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG L 3 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG L 3 " 0.535 2.00e-02 2.50e+03 pdb=" O7 NAG L 3 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A1306 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.050 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.309 2.00e-02 2.50e+03 2.58e-01 8.30e+02 pdb=" C7 NAG A1303 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.198 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.436 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " -0.014 2.00e-02 2.50e+03 ... (remaining 1340 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 319 2.72 - 3.27: 7841 3.27 - 3.81: 12308 3.81 - 4.36: 16124 4.36 - 4.90: 27300 Nonbonded interactions: 63892 Sorted by model distance: nonbonded pdb=" OE1 GLU A 624 " pdb=" OG SER A 881 " model vdw 2.180 2.440 nonbonded pdb=" OD2 ASP A 534 " pdb=" OG1 THR A 536 " model vdw 2.189 2.440 nonbonded pdb=" O ALA A 365 " pdb=" OH TYR A 689 " model vdw 2.192 2.440 nonbonded pdb=" OE1 GLU A 374 " pdb=" OG SER A 688 " model vdw 2.256 2.440 nonbonded pdb=" OD1 ASP A 712 " pdb=" OG1 THR A1219 " model vdw 2.274 2.440 ... (remaining 63887 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 'L' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 7.720 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.410 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:16.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.006 0.078 8115 Z= 0.424 Angle : 0.974 18.663 11075 Z= 0.485 Chirality : 0.057 0.312 1339 Planarity : 0.017 0.300 1333 Dihedral : 14.888 141.933 2819 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.00 % 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: -3.11 (0.21), residues: 955 helix: -2.13 (0.15), residues: 534 sheet: -0.21 (0.67), residues: 62 loop : -2.04 (0.29), residues: 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.887 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 77 average time/residue: 1.0958 time to fit residues: 90.7523 Evaluate side-chains 58 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.0497 time to fit residues: 2.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 873 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8115 Z= 0.190 Angle : 0.625 9.667 11075 Z= 0.289 Chirality : 0.044 0.267 1339 Planarity : 0.004 0.039 1333 Dihedral : 10.357 117.864 1126 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.25), residues: 955 helix: -0.18 (0.21), residues: 529 sheet: 0.10 (0.67), residues: 62 loop : -1.65 (0.30), residues: 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.973 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 68 average time/residue: 1.1532 time to fit residues: 84.1735 Evaluate side-chains 59 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 4 average time/residue: 0.8828 time to fit residues: 5.0141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 0.0370 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8115 Z= 0.199 Angle : 0.590 9.335 11075 Z= 0.275 Chirality : 0.043 0.258 1339 Planarity : 0.003 0.035 1333 Dihedral : 9.463 112.586 1126 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.27), residues: 955 helix: 0.45 (0.23), residues: 526 sheet: 0.20 (0.68), residues: 62 loop : -1.42 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.920 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 60 average time/residue: 1.0965 time to fit residues: 71.5007 Evaluate side-chains 51 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.816 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 1.0560 time to fit residues: 2.2663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS A 722 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8115 Z= 0.212 Angle : 0.591 9.418 11075 Z= 0.274 Chirality : 0.043 0.259 1339 Planarity : 0.003 0.031 1333 Dihedral : 9.048 106.787 1126 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 1.48 % 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: -0.16 (0.28), residues: 955 helix: 0.73 (0.23), residues: 524 sheet: 0.20 (0.69), residues: 62 loop : -1.35 (0.32), residues: 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.908 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.9607 time to fit residues: 60.7363 Evaluate side-chains 54 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.5723 time to fit residues: 2.4543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8115 Z= 0.262 Angle : 0.618 9.539 11075 Z= 0.288 Chirality : 0.044 0.265 1339 Planarity : 0.003 0.031 1333 Dihedral : 8.764 102.755 1126 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 1.85 % 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: -0.22 (0.28), residues: 955 helix: 0.70 (0.23), residues: 527 sheet: 0.20 (0.69), residues: 62 loop : -1.43 (0.32), residues: 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.899 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 62 average time/residue: 0.9701 time to fit residues: 65.4933 Evaluate side-chains 56 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.5443 time to fit residues: 2.3968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 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 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8115 Z= 0.208 Angle : 0.587 9.616 11075 Z= 0.273 Chirality : 0.043 0.264 1339 Planarity : 0.003 0.030 1333 Dihedral : 8.430 100.053 1126 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.28), residues: 955 helix: 0.80 (0.23), residues: 531 sheet: 0.05 (0.65), residues: 68 loop : -1.37 (0.33), residues: 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.888 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.9834 time to fit residues: 65.3470 Evaluate side-chains 57 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.7035 time to fit residues: 3.4508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.0670 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8115 Z= 0.171 Angle : 0.566 9.610 11075 Z= 0.263 Chirality : 0.041 0.262 1339 Planarity : 0.003 0.029 1333 Dihedral : 8.159 96.656 1126 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.28), residues: 955 helix: 1.01 (0.24), residues: 527 sheet: 0.10 (0.66), residues: 68 loop : -1.30 (0.33), residues: 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.878 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.9273 time to fit residues: 64.9271 Evaluate side-chains 61 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0787 time to fit residues: 1.3228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8115 Z= 0.196 Angle : 0.578 9.976 11075 Z= 0.269 Chirality : 0.042 0.264 1339 Planarity : 0.003 0.029 1333 Dihedral : 8.143 94.049 1126 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 1.97 % 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: 0.12 (0.28), residues: 955 helix: 1.05 (0.24), residues: 526 sheet: 0.10 (0.66), residues: 68 loop : -1.36 (0.33), residues: 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 64 average time/residue: 0.9290 time to fit residues: 65.3657 Evaluate side-chains 63 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0738 time to fit residues: 1.4343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8115 Z= 0.200 Angle : 0.585 10.112 11075 Z= 0.272 Chirality : 0.042 0.258 1339 Planarity : 0.003 0.029 1333 Dihedral : 7.998 92.371 1126 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 1.48 % 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: 0.14 (0.28), residues: 955 helix: 1.02 (0.23), residues: 531 sheet: 0.12 (0.66), residues: 68 loop : -1.32 (0.33), residues: 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.9467 time to fit residues: 69.4067 Evaluate side-chains 60 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0873 time to fit residues: 1.3434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8115 Z= 0.182 Angle : 0.570 10.170 11075 Z= 0.264 Chirality : 0.041 0.251 1339 Planarity : 0.003 0.028 1333 Dihedral : 7.829 91.092 1126 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.23 % 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: 0.22 (0.28), residues: 955 helix: 1.09 (0.24), residues: 528 sheet: 0.15 (0.66), residues: 68 loop : -1.27 (0.33), residues: 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.9228 time to fit residues: 62.5826 Evaluate side-chains 59 residues out of total 813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0745 time to fit residues: 1.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.0000 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101401 restraints weight = 11147.045| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.99 r_work: 0.3121 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8115 Z= 0.190 Angle : 0.583 10.325 11075 Z= 0.270 Chirality : 0.042 0.247 1339 Planarity : 0.003 0.028 1333 Dihedral : 7.773 90.615 1126 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 1.35 % 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: 0.22 (0.28), residues: 955 helix: 1.10 (0.24), residues: 528 sheet: 0.14 (0.66), residues: 68 loop : -1.27 (0.33), residues: 359 =============================================================================== Job complete usr+sys time: 2256.63 seconds wall clock time: 41 minutes 8.10 seconds (2468.10 seconds total)