Starting phenix.real_space_refine on Sat Sep 12 06:13:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_33957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_33957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_33957.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_33957.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_33957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_33957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynb_33957/09_2026/7ynb_33957.map" } resolution = 3.46 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 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: {'RNAv2': 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: 3.08, per 1000 atoms: 0.22 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: 1.15 Conformation dependent library (CDL) restraints added in 692.2 milliseconds 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: 1.82 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: 3.40 Time building geometry restraints manager: 1.56 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: 18704 1.78 - 3.55: 747 3.55 - 5.33: 122 5.33 - 7.11: 16 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: 8057 31.68 - 63.36: 434 63.36 - 95.05: 44 95.05 - 126.73: 0 126.73 - 158.41: 2 Dihedral angle restraints: 8537 sinusoidal: 4106 harmonic: 4431 Sorted by residual: dihedral pdb=" C4' U C 7 " pdb=" C3' U C 7 " pdb=" C2' U C 7 " pdb=" C1' U C 7 " ideal model delta sinusoidal sigma weight residual 36.34 -38.52 74.86 1 3.10e+00 1.04e-01 7.38e+02 dihedral pdb=" C4' A B 10 " pdb=" C3' A B 10 " pdb=" C2' A B 10 " pdb=" C1' A B 10 " ideal model delta sinusoidal sigma weight residual 36.34 -37.64 73.98 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' C B 15 " pdb=" C3' C B 15 " pdb=" C2' C B 15 " pdb=" C1' C B 15 " ideal model delta sinusoidal sigma weight residual 36.34 -37.59 73.94 1 3.10e+00 1.04e-01 7.23e+02 ... (remaining 8534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1669 0.063 - 0.126: 286 0.126 - 0.189: 37 0.189 - 0.252: 70 0.252 - 0.315: 37 Chirality restraints: 2099 Sorted by residual: chirality pdb=" C3' A B 5 " pdb=" C4' A B 5 " pdb=" O3' A B 5 " pdb=" C2' A B 5 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3' U C 7 " pdb=" C4' U C 7 " pdb=" O3' U C 7 " pdb=" C2' U C 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" P G B -13 " pdb=" OP1 G B -13 " pdb=" OP2 G B -13 " pdb=" O5' G B -13 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.26e+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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 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= 0.228 Angle : 0.810 8.885 19593 Z= 0.441 Chirality : 0.072 0.315 2099 Planarity : 0.006 0.074 2318 Dihedral : 18.359 158.408 5679 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG A 967 TYR 0.010 0.001 TYR A1147 PHE 0.014 0.002 PHE A 528 TRP 0.024 0.001 TRP A1600 HIS 0.006 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (14307) covalent geometry : angle 0.81007 / 0.44 (19593) hydrogen bonds : bond 0.21250 / 12.71 ( 339) hydrogen bonds : angle 6.99251 / 5.09 ( 952) *********************** 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 : 0.416 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: 0.1590 time to fit residues: 25.8970 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 : 0.414 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 456 GLN A 464 ASN A 531 GLN A 985 ASN A1095 HIS A1127 GLN A1417 HIS A1483 HIS A1514 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080133 restraints weight = 26215.456| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.43 r_work: 0.2900 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14307 Z= 0.162 Angle : 0.934 13.767 19593 Z= 0.417 Chirality : 0.086 0.898 2099 Planarity : 0.006 0.064 2318 Dihedral : 14.569 153.766 2482 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 1.56 % Allowed : 14.06 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.19), residues: 1526 helix: -0.22 (0.30), residues: 308 sheet: -1.39 (0.29), residues: 270 loop : -3.54 (0.15), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1193 TYR 0.008 0.001 TYR A1209 PHE 0.026 0.001 PHE A1073 TRP 0.016 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (14307) covalent geometry : angle 0.93395 / 0.42 (19593) hydrogen bonds : bond 0.04354 / 2.80 ( 339) hydrogen bonds : angle 4.73440 / 3.42 ( 952) *********************** 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 94 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1097 TRP cc_start: 0.8910 (m-10) cc_final: 0.8264 (m100) REVERT: A 1211 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7432 (tmm) outliers start: 21 outliers final: 12 residues processed: 91 average time/residue: 0.1033 time to fit residues: 14.3976 Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 950 LEU 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 118 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.074681 restraints weight = 26767.110| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.55 r_work: 0.2795 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14307 Z= 0.241 Angle : 0.886 11.298 19593 Z= 0.417 Chirality : 0.083 0.960 2099 Planarity : 0.006 0.064 2318 Dihedral : 14.815 168.901 2471 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 1.71 % Allowed : 16.22 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.19), residues: 1526 helix: 0.63 (0.32), residues: 304 sheet: -1.33 (0.29), residues: 287 loop : -3.41 (0.16), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 470 TYR 0.013 0.002 TYR A1276 PHE 0.022 0.002 PHE A1083 TRP 0.019 0.001 TRP A1600 HIS 0.005 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (14307) covalent geometry : angle 0.88555 / 0.42 (19593) hydrogen bonds : bond 0.05111 / 3.36 ( 339) hydrogen bonds : angle 4.50276 / 3.24 ( 952) *********************** 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 81 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1211 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7835 (tmm) outliers start: 23 outliers final: 16 residues processed: 77 average time/residue: 0.1022 time to fit residues: 12.5000 Evaluate side-chains 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS 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 504 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 900 ILE 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 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 148 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS A 344 ASN A1418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077887 restraints weight = 26586.117| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.44 r_work: 0.2855 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14307 Z= 0.157 Angle : 0.793 11.241 19593 Z= 0.367 Chirality : 0.074 0.774 2099 Planarity : 0.005 0.063 2318 Dihedral : 14.698 173.880 2471 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.31 % Allowed : 16.89 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.20), residues: 1526 helix: 1.06 (0.33), residues: 304 sheet: -0.85 (0.31), residues: 268 loop : -3.24 (0.16), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.009 0.001 TYR A 313 PHE 0.017 0.001 PHE A1073 TRP 0.018 0.001 TRP A1600 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (14307) covalent geometry : angle 0.79342 / 0.37 (19593) hydrogen bonds : bond 0.03832 / 2.52 ( 339) hydrogen bonds : angle 4.24423 / 3.05 ( 952) *********************** 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 88 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7265 (tpp80) REVERT: A 1211 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7756 (tmm) outliers start: 31 outliers final: 19 residues processed: 82 average time/residue: 0.0991 time to fit residues: 12.8699 Evaluate side-chains 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN 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 382 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 742 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 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 Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 57 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1280 ASN A1428 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.075433 restraints weight = 26778.036| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.54 r_work: 0.2816 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14307 Z= 0.197 Angle : 0.819 11.924 19593 Z= 0.383 Chirality : 0.076 0.878 2099 Planarity : 0.005 0.064 2318 Dihedral : 14.686 169.672 2471 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 2.60 % Allowed : 17.71 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.20), residues: 1526 helix: 1.26 (0.33), residues: 305 sheet: -1.05 (0.30), residues: 288 loop : -3.12 (0.16), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 645 TYR 0.010 0.001 TYR A1276 PHE 0.020 0.002 PHE A1073 TRP 0.018 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (14307) covalent geometry : angle 0.81852 / 0.38 (19593) hydrogen bonds : bond 0.04396 / 2.90 ( 339) hydrogen bonds : angle 4.23983 / 3.04 ( 952) *********************** REFINEMENT MACRO_CYCLE 5 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: 35 poor density : 55 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1211 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.7883 (tmm) outliers start: 35 outliers final: 20 residues processed: 82 average time/residue: 0.0952 time to fit residues: 12.5750 Evaluate side-chains 74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN 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 382 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 742 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 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1305 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.074735 restraints weight = 26804.707| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.42 r_work: 0.2809 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14307 Z= 0.230 Angle : 0.839 11.830 19593 Z= 0.394 Chirality : 0.079 0.987 2099 Planarity : 0.005 0.065 2318 Dihedral : 14.772 167.694 2471 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 2.38 % Allowed : 18.75 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.20), residues: 1526 helix: 1.24 (0.33), residues: 305 sheet: -1.06 (0.30), residues: 291 loop : -3.10 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 448 TYR 0.012 0.001 TYR A1276 PHE 0.018 0.002 PHE A1073 TRP 0.019 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (14307) covalent geometry : angle 0.83925 / 0.39 (19593) hydrogen bonds : bond 0.04617 / 3.04 ( 339) hydrogen bonds : angle 4.30002 / 3.07 ( 952) *********************** REFINEMENT MACRO_CYCLE 6 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 86 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1211 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: A 1269 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8587 (tt) outliers start: 32 outliers final: 22 residues processed: 80 average time/residue: 0.0972 time to fit residues: 12.4443 Evaluate side-chains 78 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN 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 504 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 950 LEU 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 1269 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1305 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 0.0070 chunk 32 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.080115 restraints weight = 26512.883| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.42 r_work: 0.2898 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14307 Z= 0.117 Angle : 0.730 10.946 19593 Z= 0.336 Chirality : 0.067 0.746 2099 Planarity : 0.005 0.063 2318 Dihedral : 14.737 176.290 2471 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 1.93 % Allowed : 19.05 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.21), residues: 1526 helix: 1.58 (0.33), residues: 302 sheet: -0.49 (0.32), residues: 263 loop : -2.92 (0.17), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1193 TYR 0.011 0.001 TYR A1081 PHE 0.017 0.001 PHE A1073 TRP 0.017 0.001 TRP A1600 HIS 0.004 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14307) covalent geometry : angle 0.73034 / 0.34 (19593) hydrogen bonds : bond 0.03098 / 2.01 ( 339) hydrogen bonds : angle 3.99568 / 2.86 ( 952) *********************** REFINEMENT MACRO_CYCLE 7 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: 26 poor density : 59 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7029 (tpp80) REVERT: A 1115 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: A 1211 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.7853 (tmm) outliers start: 26 outliers final: 15 residues processed: 79 average time/residue: 0.1081 time to fit residues: 13.3436 Evaluate side-chains 73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 837 PHE 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 1115 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.100559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.074373 restraints weight = 26751.304| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.43 r_work: 0.2781 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14307 Z= 0.245 Angle : 0.845 12.332 19593 Z= 0.397 Chirality : 0.079 1.001 2099 Planarity : 0.005 0.065 2318 Dihedral : 14.707 165.767 2470 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 1.93 % Allowed : 19.27 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.21), residues: 1526 helix: 1.56 (0.33), residues: 300 sheet: -0.99 (0.30), residues: 290 loop : -2.95 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 290 TYR 0.018 0.002 TYR A1081 PHE 0.017 0.002 PHE A 747 TRP 0.017 0.001 TRP A1600 HIS 0.005 0.001 HIS A1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 (14307) covalent geometry : angle 0.84471 / 0.40 (19593) hydrogen bonds : bond 0.04850 / 3.18 ( 339) hydrogen bonds : angle 4.28801 / 3.06 ( 952) *********************** REFINEMENT MACRO_CYCLE 8 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 81 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7084 (tpp80) REVERT: A 1115 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: A 1211 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8041 (tmm) REVERT: A 1269 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8635 (tt) outliers start: 26 outliers final: 18 residues processed: 75 average time/residue: 0.1055 time to fit residues: 12.3549 Evaluate side-chains 76 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN 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 490 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 742 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 1115 GLU 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 1269 LEU Chi-restraints excluded: chain A residue 1295 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 16 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.076041 restraints weight = 26744.753| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.41 r_work: 0.2823 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14307 Z= 0.185 Angle : 0.790 11.691 19593 Z= 0.368 Chirality : 0.074 0.879 2099 Planarity : 0.005 0.066 2318 Dihedral : 14.771 168.838 2470 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 2.01 % Allowed : 19.64 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.21), residues: 1526 helix: 1.56 (0.33), residues: 301 sheet: -0.63 (0.31), residues: 263 loop : -2.91 (0.17), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 448 TYR 0.015 0.001 TYR A1081 PHE 0.016 0.001 PHE A 747 TRP 0.018 0.001 TRP A1600 HIS 0.004 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (14307) covalent geometry : angle 0.78958 / 0.37 (19593) hydrogen bonds : bond 0.04068 / 2.66 ( 339) hydrogen bonds : angle 4.16421 / 2.98 ( 952) *********************** REFINEMENT MACRO_CYCLE 9 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 83 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7190 (tpp80) REVERT: A 1115 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: A 1211 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8080 (tmm) REVERT: A 1269 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8620 (tt) REVERT: A 1375 LYS cc_start: 0.8638 (ptmt) cc_final: 0.8412 (pttt) outliers start: 27 outliers final: 21 residues processed: 78 average time/residue: 0.1002 time to fit residues: 12.2375 Evaluate side-chains 81 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN 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 361 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 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 1115 GLU 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 1269 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1510 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 127 optimal weight: 0.3980 chunk 143 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.080086 restraints weight = 26549.072| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.43 r_work: 0.2906 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14307 Z= 0.122 Angle : 0.721 10.953 19593 Z= 0.332 Chirality : 0.066 0.751 2099 Planarity : 0.005 0.065 2318 Dihedral : 14.707 176.833 2470 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 1.56 % Allowed : 20.16 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.21), residues: 1526 helix: 1.81 (0.33), residues: 301 sheet: -0.49 (0.32), residues: 256 loop : -2.78 (0.17), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 917 TYR 0.015 0.001 TYR A1081 PHE 0.015 0.001 PHE A1073 TRP 0.016 0.001 TRP A1600 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14307) covalent geometry : angle 0.72058 / 0.33 (19593) hydrogen bonds : bond 0.03105 / 2.02 ( 339) hydrogen bonds : angle 3.93684 / 2.81 ( 952) ********************** REFINEMENT MACRO_CYCLE 10 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 83 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6948 (tpp80) REVERT: A 1115 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: A 1211 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.7930 (tmm) REVERT: A 1375 LYS cc_start: 0.8637 (ptmt) cc_final: 0.8402 (pttt) outliers start: 21 outliers final: 18 residues processed: 79 average time/residue: 0.1090 time to fit residues: 13.3003 Evaluate side-chains 78 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN 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 361 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 742 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 1115 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 87 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 135 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.078451 restraints weight = 26605.202| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.41 r_work: 0.2868 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14307 Z= 0.149 Angle : 0.738 11.544 19593 Z= 0.342 Chirality : 0.068 0.772 2099 Planarity : 0.005 0.065 2318 Dihedral : 14.634 173.016 2470 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 1.86 % Allowed : 19.79 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.21), residues: 1526 helix: 1.80 (0.33), residues: 307 sheet: -0.41 (0.32), residues: 249 loop : -2.75 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.014 0.001 TYR A1081 PHE 0.014 0.001 PHE A1073 TRP 0.017 0.001 TRP A1600 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14307) covalent geometry : angle 0.73785 / 0.34 (19593) hydrogen bonds : bond 0.03596 / 2.36 ( 339) hydrogen bonds : angle 3.97798 / 2.84 ( 952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3078.58 seconds wall clock time: 53 minutes 39.53 seconds (3219.53 seconds total)