Starting phenix.real_space_refine on Thu Jun 12 18:05:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynb_33957/06_2025/7ynb_33957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynb_33957/06_2025/7ynb_33957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ynb_33957/06_2025/7ynb_33957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynb_33957/06_2025/7ynb_33957.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynb_33957/06_2025/7ynb_33957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynb_33957/06_2025/7ynb_33957.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 66 5.49 5 S 57 5.16 5 C 8496 2.51 5 N 2463 2.21 5 O 2765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13847 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1536, 12447 Classifications: {'peptide': 1536} Link IDs: {'PTRANS': 84, 'TRANS': 1451} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 5, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "C" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 590 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 23} Time building chain proxies: 8.91, per 1000 atoms: 0.64 Number of scatterers: 13847 At special positions: 0 Unit cell: (93.09, 171.2, 132.68, 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 57 16.00 P 66 15.00 O 2765 8.00 N 2463 7.00 C 8496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 18 sheets defined 21.5% alpha, 19.6% beta 14 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 57 through 74 removed outlier: 4.170A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.547A pdb=" N ASN A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 295 removed outlier: 4.106A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 295 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 295' Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.804A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.010A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.659A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.675A pdb=" N GLY A 566 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.219A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.720A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.630A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.774A pdb=" N GLU A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 784' Processing helix chain 'A' and resid 787 through 801 removed outlier: 3.727A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.623A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 813' Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.257A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 3.976A pdb=" N GLU A1106 " --> pdb=" O ASN A1102 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.912A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.631A pdb=" N LYS A1303 " --> pdb=" O MET A1300 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A1304 " --> pdb=" O ILE A1301 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1300 through 1305' Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.880A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1476 Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1595 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.689A pdb=" N PHE A 187 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 189 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 191 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 169 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.520A pdb=" N GLY A 408 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 403 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 576 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.769A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 723 through 724 removed outlier: 6.766A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.637A pdb=" N PHE A 757 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB1, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.446A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB3, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB4, first strand: chain 'A' and resid 1001 through 1012 removed outlier: 42.247A pdb=" N ILE A1002 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 35.571A pdb=" N ASP A1123 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 30.308A pdb=" N LYS A1004 " --> pdb=" O ASP A1123 " (cutoff:3.500A) removed outlier: 24.624A pdb=" N ARG A1125 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 19.697A pdb=" N SER A1006 " --> pdb=" O ARG A1125 " (cutoff:3.500A) removed outlier: 14.161A pdb=" N GLN A1127 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR A1008 " --> pdb=" O GLN A1127 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A1047 " --> pdb=" O TRP A1120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A1122 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A1130 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N MET A1037 " --> pdb=" O PHE A1130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A1037 " --> pdb=" O LYS A1144 " (cutoff:3.500A) removed outlier: 19.248A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.076A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A1149 " --> pdb=" O THR A1217 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR A1217 " --> pdb=" O HIS A1149 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A1283 " --> pdb=" O ASN A1280 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A1284 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU A1229 " --> pdb=" O VAL A1284 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP A1286 " --> pdb=" O GLU A1229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1086 removed outlier: 3.601A pdb=" N PHE A1083 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1096 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A1085 " --> pdb=" O PHE A1094 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A1094 " --> pdb=" O VAL A1085 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 3.556A pdb=" N ASP A1187 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1200 through 1202 Processing sheet with id=AB9, first strand: chain 'A' and resid 1385 through 1387 310 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 6.59 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4107 1.33 - 1.45: 2769 1.45 - 1.57: 7219 1.57 - 1.70: 130 1.70 - 1.82: 82 Bond restraints: 14307 Sorted by residual: bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.53e+00 bond pdb=" N CYS A 86 " pdb=" CA CYS A 86 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.98e+00 bond pdb=" N CYS A1342 " pdb=" CA CYS A1342 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.41e-02 5.03e+03 6.69e+00 bond pdb=" N CYS A1345 " pdb=" CA CYS A1345 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.26e-02 6.30e+03 6.22e+00 bond pdb=" N CYS A 708 " pdb=" CA CYS A 708 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.37e-02 5.33e+03 5.70e+00 ... (remaining 14302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 18953 1.78 - 3.55: 562 3.55 - 5.33: 62 5.33 - 7.11: 12 7.11 - 8.88: 4 Bond angle restraints: 19593 Sorted by residual: angle pdb=" N ARG A1346 " pdb=" CA ARG A1346 " pdb=" C ARG A1346 " ideal model delta sigma weight residual 113.88 108.17 5.71 1.23e+00 6.61e-01 2.15e+01 angle pdb=" N TYR A 866 " pdb=" CA TYR A 866 " pdb=" C TYR A 866 " ideal model delta sigma weight residual 111.02 116.25 -5.23 1.25e+00 6.40e-01 1.75e+01 angle pdb=" C LYS A1107 " pdb=" N LEU A1108 " pdb=" CA LEU A1108 " ideal model delta sigma weight residual 120.44 125.26 -4.82 1.30e+00 5.92e-01 1.38e+01 angle pdb=" N CYS A 123 " pdb=" CA CYS A 123 " pdb=" C CYS A 123 " ideal model delta sigma weight residual 110.07 105.83 4.24 1.26e+00 6.30e-01 1.13e+01 angle pdb=" C LEU A1108 " pdb=" N GLU A1109 " pdb=" CA GLU A1109 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 ... (remaining 19588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 8264 31.68 - 63.36: 424 63.36 - 95.05: 58 95.05 - 126.73: 5 126.73 - 158.41: 2 Dihedral angle restraints: 8753 sinusoidal: 4322 harmonic: 4431 Sorted by residual: dihedral pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " pdb=" C1' A C -2 " ideal model delta sinusoidal sigma weight residual -35.00 32.58 -67.58 1 8.00e+00 1.56e-02 9.28e+01 dihedral pdb=" C5' A C -2 " pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" O3' A C -2 " ideal model delta sinusoidal sigma weight residual 147.00 82.03 64.97 1 8.00e+00 1.56e-02 8.65e+01 dihedral pdb=" O4' A C -2 " pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " ideal model delta sinusoidal sigma weight residual 24.00 -33.84 57.84 1 8.00e+00 1.56e-02 7.02e+01 ... (remaining 8750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1683 0.055 - 0.110: 350 0.110 - 0.165: 61 0.165 - 0.220: 4 0.220 - 0.275: 1 Chirality restraints: 2099 Sorted by residual: chirality pdb=" C3' A C -2 " pdb=" C4' A C -2 " pdb=" O3' A C -2 " pdb=" C2' A C -2 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' A C -2 " pdb=" C3' A C -2 " pdb=" O2' A C -2 " pdb=" C1' A C -2 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA CYS A 123 " pdb=" N CYS A 123 " pdb=" C CYS A 123 " pdb=" CB CYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2096 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 435 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO A 436 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO A 864 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 636 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 637 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 637 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 637 " -0.034 5.00e-02 4.00e+02 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 433 2.68 - 3.24: 12020 3.24 - 3.79: 20015 3.79 - 4.35: 26513 4.35 - 4.90: 44920 Nonbonded interactions: 103901 Sorted by model distance: nonbonded pdb=" O2' A B 11 " pdb=" O4' C B 12 " model vdw 2.127 3.040 nonbonded pdb=" OE1 GLU A 70 " pdb=" NH2 ARG A 104 " model vdw 2.254 3.120 nonbonded pdb=" OG SER A1006 " pdb=" OD1 ASP A1221 " model vdw 2.257 3.040 nonbonded pdb=" NH2 ARG A 917 " pdb=" O GLU A 922 " model vdw 2.274 3.120 nonbonded pdb=" N ASP A1404 " pdb=" OD1 ASP A1404 " model vdw 2.286 3.120 ... (remaining 103896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.540 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.005 0.046 14307 Z= 0.225 Angle : 0.719 8.885 19593 Z= 0.423 Chirality : 0.047 0.275 2099 Planarity : 0.006 0.074 2318 Dihedral : 18.406 158.408 5895 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.01 % Favored : 88.79 % Rotamer: Outliers : 1.26 % Allowed : 11.38 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.52 (0.17), residues: 1526 helix: -1.93 (0.25), residues: 306 sheet: -2.04 (0.28), residues: 282 loop : -3.94 (0.14), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1600 HIS 0.006 0.001 HIS A1279 PHE 0.014 0.002 PHE A 528 TYR 0.010 0.001 TYR A1147 ARG 0.005 0.001 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.21250 ( 339) hydrogen bonds : angle 6.99251 ( 952) covalent geometry : bond 0.00483 (14307) covalent geometry : angle 0.71859 (19593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 120 average time/residue: 0.3776 time to fit residues: 62.0004 Evaluate side-chains 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 1105 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1404 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN A 464 ASN A 531 GLN A 985 ASN A1095 HIS A1127 GLN A1248 ASN A1417 HIS A1418 HIS A1483 HIS A1514 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.071990 restraints weight = 26296.377| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.53 r_work: 0.2747 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14307 Z= 0.228 Angle : 0.685 9.803 19593 Z= 0.362 Chirality : 0.047 0.204 2099 Planarity : 0.006 0.070 2318 Dihedral : 16.474 163.389 2698 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 1.56 % Allowed : 15.10 % Favored : 83.33 % 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: -3.51 (0.19), residues: 1526 helix: -0.11 (0.31), residues: 308 sheet: -1.67 (0.28), residues: 286 loop : -3.57 (0.15), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 PHE 0.028 0.002 PHE A1073 TYR 0.014 0.002 TYR A1276 ARG 0.006 0.001 ARG A1193 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 339) hydrogen bonds : angle 4.72140 ( 952) covalent geometry : bond 0.00540 (14307) covalent geometry : angle 0.68494 (19593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 ASP cc_start: 0.7593 (t70) cc_final: 0.7317 (t70) REVERT: A 1097 TRP cc_start: 0.8974 (m-10) cc_final: 0.8159 (m100) REVERT: A 1211 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7696 (tmm) outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 0.2440 time to fit residues: 31.8891 Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1022 ASP Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 17 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 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 118 ASN A 344 ASN A1428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.070802 restraints weight = 26425.214| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.52 r_work: 0.2727 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14307 Z= 0.222 Angle : 0.659 10.113 19593 Z= 0.347 Chirality : 0.046 0.204 2099 Planarity : 0.006 0.063 2318 Dihedral : 16.305 161.996 2687 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 2.46 % Allowed : 16.89 % Favored : 80.65 % 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: -2.99 (0.19), residues: 1526 helix: 0.77 (0.32), residues: 304 sheet: -1.39 (0.29), residues: 287 loop : -3.37 (0.16), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 PHE 0.020 0.002 PHE A1073 TYR 0.012 0.001 TYR A1276 ARG 0.005 0.000 ARG A 917 Details of bonding type rmsd hydrogen bonds : bond 0.05011 ( 339) hydrogen bonds : angle 4.48000 ( 952) covalent geometry : bond 0.00529 (14307) covalent geometry : angle 0.65875 (19593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1211 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.7871 (tmm) outliers start: 33 outliers final: 19 residues processed: 86 average time/residue: 0.2319 time to fit residues: 32.0471 Evaluate side-chains 74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1022 ASP Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 25 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.074830 restraints weight = 26239.547| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.50 r_work: 0.2812 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14307 Z= 0.118 Angle : 0.566 11.244 19593 Z= 0.293 Chirality : 0.042 0.201 2099 Planarity : 0.005 0.062 2318 Dihedral : 16.200 164.457 2687 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.31 % Allowed : 17.19 % Favored : 80.51 % 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: -2.54 (0.20), residues: 1526 helix: 1.41 (0.33), residues: 295 sheet: -0.97 (0.30), residues: 272 loop : -3.15 (0.16), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1600 HIS 0.005 0.001 HIS A1279 PHE 0.018 0.001 PHE A1073 TYR 0.019 0.001 TYR A1081 ARG 0.008 0.000 ARG A 470 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 339) hydrogen bonds : angle 4.10972 ( 952) covalent geometry : bond 0.00275 (14307) covalent geometry : angle 0.56633 (19593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7153 (tpp80) REVERT: A 1211 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7777 (tmm) outliers start: 31 outliers final: 16 residues processed: 85 average time/residue: 0.2615 time to fit residues: 34.3489 Evaluate side-chains 76 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 692 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6269 > 50: distance: 56 - 66: 18.356 distance: 66 - 67: 21.554 distance: 67 - 68: 13.930 distance: 67 - 70: 11.800 distance: 68 - 69: 24.112 distance: 68 - 74: 26.954 distance: 70 - 71: 3.354 distance: 71 - 72: 14.229 distance: 71 - 73: 27.949 distance: 74 - 75: 16.876 distance: 75 - 76: 13.406 distance: 75 - 78: 6.920 distance: 76 - 77: 6.280 distance: 76 - 88: 7.690 distance: 78 - 79: 4.630 distance: 79 - 80: 13.401 distance: 79 - 81: 8.251 distance: 80 - 82: 12.458 distance: 81 - 83: 7.406 distance: 82 - 83: 3.293 distance: 83 - 85: 4.715 distance: 84 - 86: 4.897 distance: 86 - 87: 10.830 distance: 88 - 89: 12.414 distance: 89 - 90: 7.466 distance: 89 - 92: 10.926 distance: 90 - 91: 9.515 distance: 90 - 96: 12.177 distance: 92 - 93: 8.499 distance: 93 - 94: 10.439 distance: 93 - 95: 9.289 distance: 96 - 97: 8.257 distance: 97 - 98: 6.812 distance: 97 - 100: 3.462 distance: 98 - 99: 11.611 distance: 98 - 104: 8.366 distance: 100 - 101: 9.111 distance: 100 - 102: 7.265 distance: 101 - 103: 9.472 distance: 104 - 105: 16.683 distance: 105 - 106: 30.264 distance: 106 - 107: 25.659 distance: 106 - 108: 23.296 distance: 108 - 109: 15.646 distance: 109 - 110: 40.457 distance: 109 - 112: 12.239 distance: 110 - 111: 28.310 distance: 110 - 117: 26.241 distance: 112 - 113: 12.970 distance: 113 - 114: 8.888 distance: 114 - 115: 5.402 distance: 115 - 116: 11.083 distance: 117 - 118: 8.118 distance: 118 - 119: 11.725 distance: 118 - 121: 12.711 distance: 119 - 120: 15.946 distance: 119 - 126: 10.411 distance: 121 - 122: 5.028 distance: 122 - 123: 11.022 distance: 123 - 124: 17.030 distance: 124 - 125: 22.793 distance: 126 - 127: 3.677 distance: 127 - 128: 3.202 distance: 127 - 130: 8.914 distance: 128 - 129: 5.557 distance: 130 - 131: 7.958 distance: 131 - 132: 10.433 distance: 132 - 133: 7.472 distance: 133 - 134: 5.760 distance: 135 - 136: 3.846 distance: 136 - 137: 7.598 distance: 136 - 139: 8.972 distance: 137 - 138: 17.447 distance: 137 - 144: 11.556 distance: 139 - 140: 10.435 distance: 140 - 141: 3.900 distance: 141 - 142: 3.176 distance: 144 - 145: 5.471 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