Starting phenix.real_space_refine (version: dev) on Sat Feb 25 21:46:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2023/7smp_25204_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2023/7smp_25204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2023/7smp_25204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2023/7smp_25204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2023/7smp_25204_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7smp_25204/02_2023/7smp_25204_trim_updated.pdb" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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 Process input model Symmetric amino acids flipped Residue "A GLU 924": "OE1" <-> "OE2" Residue "A GLU 1158": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26477 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 13184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 13184 Classifications: {'peptide': 833} Link IDs: {'PTRANS': 29, 'TRANS': 803} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 13216 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 29, 'TRANS': 805} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' K': 1, '82U': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' K': 1, '82U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.25, per 1000 atoms: 0.46 Number of scatterers: 26477 At special positions: 0 Unit cell: (84.53, 151.94, 124.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 83 16.00 O 2318 8.00 N 2148 7.00 C 8573 6.00 H 13353 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.04 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 3 sheets defined 57.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'B' and resid 287 through 290 No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 292 through 299 Processing helix chain 'B' and resid 302 through 305 No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 317 through 342 Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 362 through 397 removed outlier: 3.619A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 428 through 454 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 487 through 497 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 514 through 543 Proline residue: B 519 - end of helix Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 592 through 596 Processing helix chain 'B' and resid 600 through 632 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 652 through 668 Processing helix chain 'B' and resid 675 through 698 Processing helix chain 'B' and resid 713 through 730 Processing helix chain 'B' and resid 732 through 751 removed outlier: 3.625A pdb=" N LEU B 736 " --> pdb=" O TRP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 779 Processing helix chain 'B' and resid 798 through 810 removed outlier: 3.605A pdb=" N ARG B 801 " --> pdb=" O PRO B 798 " (cutoff:3.500A) Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 828 through 848 removed outlier: 4.239A pdb=" N MET B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 834 " --> pdb=" O GLN B 830 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 873 Processing helix chain 'B' and resid 897 through 912 Processing helix chain 'B' and resid 1035 through 1044 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1065 through 1078 Processing helix chain 'B' and resid 1098 through 1111 Proline residue: B1110 - end of helix Processing helix chain 'B' and resid 1120 through 1128 Processing helix chain 'B' and resid 1136 through 1159 removed outlier: 5.682A pdb=" N THR B1144 " --> pdb=" O GLU B1140 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1190 Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 317 through 342 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 362 through 397 removed outlier: 3.648A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 removed outlier: 3.659A pdb=" N ALA A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 4.056A pdb=" N ALA A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 487 through 497 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 514 through 542 Proline residue: A 519 - end of helix removed outlier: 3.526A pdb=" N SER A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 Processing helix chain 'A' and resid 592 through 596 Processing helix chain 'A' and resid 600 through 631 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 652 through 668 Processing helix chain 'A' and resid 672 through 698 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 713 through 730 Processing helix chain 'A' and resid 732 through 751 Processing helix chain 'A' and resid 761 through 779 Processing helix chain 'A' and resid 798 through 810 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 897 through 912 Processing helix chain 'A' and resid 1035 through 1044 Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1062 through 1078 removed outlier: 5.795A pdb=" N ASP A1066 " --> pdb=" O ASN A1063 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS A1067 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1111 Proline residue: A1110 - end of helix Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1136 through 1159 removed outlier: 5.776A pdb=" N THR A1144 " --> pdb=" O GLU A1140 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1190 Processing sheet with id= A, first strand: chain 'B' and resid 791 through 793 removed outlier: 6.658A pdb=" N PHE B 854 " --> pdb=" O CYS B 820 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N HIS B 822 " --> pdb=" O PHE B 854 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 856 " --> pdb=" O HIS B 822 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS B 824 " --> pdb=" O ALA B 856 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 858 " --> pdb=" O HIS B 824 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 883 through 887 removed outlier: 6.222A pdb=" N GLY B 916 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 886 " --> pdb=" O GLY B 916 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL B 918 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP B1085 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE B1058 " --> pdb=" O ASP B1085 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N MET B1087 " --> pdb=" O ILE B1058 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1086 through 1089 removed outlier: 6.386A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1169 " --> pdb=" O TRP A1027 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N MET A1168 " --> pdb=" O PRO A1196 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A1198 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY A 887 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE A 854 " --> pdb=" O CYS A 820 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N HIS A 822 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A 856 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS A 824 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 858 " --> pdb=" O HIS A 824 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.34 Time building geometry restraints manager: 23.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13337 1.03 - 1.23: 55 1.23 - 1.42: 5511 1.42 - 1.62: 7728 1.62 - 1.82: 142 Bond restraints: 26773 Sorted by residual: bond pdb=" N 82U B1302 " pdb=" CA 82U B1302 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" N 82U A1301 " pdb=" CA 82U A1301 " ideal model delta sigma weight residual 1.366 1.433 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" N 82U B1301 " pdb=" CA 82U B1301 " ideal model delta sigma weight residual 1.366 1.432 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" NE1 82U A1301 " pdb=" S1 82U A1301 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" NE1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.34e+00 ... (remaining 26768 not shown) Histogram of bond angle deviations from ideal: 99.10 - 107.00: 583 107.00 - 114.89: 33450 114.89 - 122.79: 11726 122.79 - 130.69: 2695 130.69 - 138.59: 63 Bond angle restraints: 48517 Sorted by residual: angle pdb=" C 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 120.11 138.59 -18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" O1 82U B1302 " pdb=" S1 82U B1302 " pdb=" O2 82U B1302 " ideal model delta sigma weight residual 118.12 100.23 17.89 3.00e+00 1.11e-01 3.56e+01 angle pdb=" O1 82U A1301 " pdb=" S1 82U A1301 " pdb=" O2 82U A1301 " ideal model delta sigma weight residual 118.12 100.59 17.53 3.00e+00 1.11e-01 3.42e+01 angle pdb=" CD2 82U B1301 " pdb=" C1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 118.42 101.58 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C 82U B1302 " pdb=" C1 82U B1302 " pdb=" S1 82U B1302 " ideal model delta sigma weight residual 120.11 136.89 -16.78 3.00e+00 1.11e-01 3.13e+01 ... (remaining 48512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 9574 17.47 - 34.94: 928 34.94 - 52.41: 145 52.41 - 69.88: 29 69.88 - 87.36: 25 Dihedral angle restraints: 10701 sinusoidal: 4917 harmonic: 5784 Sorted by residual: dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 34.97 58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" C 82U A1301 " pdb=" N 82U A1301 " pdb=" CA 82U A1301 " pdb=" CB 82U A1301 " ideal model delta harmonic sigma weight residual -122.60 -137.94 15.34 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" C 82U B1301 " pdb=" N 82U B1301 " pdb=" CA 82U B1301 " pdb=" CB 82U B1301 " ideal model delta harmonic sigma weight residual -122.60 -137.90 15.30 0 2.50e+00 1.60e-01 3.75e+01 ... (remaining 10698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1387 0.034 - 0.067: 512 0.067 - 0.101: 142 0.101 - 0.134: 49 0.134 - 0.168: 2 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CG LEU B 683 " pdb=" CB LEU B 683 " pdb=" CD1 LEU B 683 " pdb=" CD2 LEU B 683 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA GLN A1149 " pdb=" N GLN A1149 " pdb=" C GLN A1149 " pdb=" CB GLN A1149 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A1086 " pdb=" N ILE A1086 " pdb=" C ILE A1086 " pdb=" CB ILE A1086 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 2089 not shown) Planarity restraints: 3862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 82U B1302 " 0.073 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" CA 82U B1302 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1302 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1302 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1302 " 0.070 2.00e-02 2.50e+03 pdb=" CG 82U B1302 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 82U B1302 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1302 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1302 " -0.001 2.00e-02 2.50e+03 pdb=" S1 82U B1302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U B1301 " 0.073 2.00e-02 2.50e+03 8.15e-02 1.66e+02 pdb=" CA 82U B1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U B1301 " 0.080 2.00e-02 2.50e+03 pdb=" O 82U B1301 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 82U B1301 " -0.000 2.00e-02 2.50e+03 pdb=" C1 82U B1301 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1301 " 0.000 2.00e-02 2.50e+03 pdb=" S1 82U B1301 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U A1301 " 0.072 2.00e-02 2.50e+03 8.13e-02 1.65e+02 pdb=" CA 82U A1301 " -0.224 2.00e-02 2.50e+03 pdb=" C 82U A1301 " 0.079 2.00e-02 2.50e+03 pdb=" O 82U A1301 " 0.006 2.00e-02 2.50e+03 pdb=" CB 82U A1301 " 0.068 2.00e-02 2.50e+03 pdb=" CG 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" C1 82U A1301 " -0.001 2.00e-02 2.50e+03 pdb=" C17 82U A1301 " 0.002 2.00e-02 2.50e+03 pdb=" S1 82U A1301 " -0.003 2.00e-02 2.50e+03 ... (remaining 3859 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 4003 2.27 - 2.98: 73560 2.98 - 3.70: 100079 3.70 - 4.42: 151609 4.42 - 5.14: 239702 Nonbonded interactions: 568953 Sorted by model distance: nonbonded pdb=" H MET B 303 " pdb=" O4 82U B1302 " model vdw 1.548 1.850 nonbonded pdb=" O ASP A 404 " pdb=" H ASP A 408 " model vdw 1.624 1.850 nonbonded pdb=" O ILE B1054 " pdb=" H SER B1084 " model vdw 1.628 1.850 nonbonded pdb=" O TRP B1132 " pdb=" HG SER B1179 " model vdw 1.629 1.850 nonbonded pdb="HD22 ASN B 506 " pdb=" OG SER B 621 " model vdw 1.645 1.850 ... (remaining 568948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 283 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 284 through 907 or (resi \ d 908 and (name N or name CA or name C or name O or name CB or name CG or name N \ D1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1 or name HE2)) or resid 909 through 1210 or resid 130 \ 1 through 1302)) selection = (chain 'B' and (resid 283 through 1210 or resid 1302 through 1303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 83 5.16 5 C 8573 2.51 5 N 2148 2.21 5 O 2318 1.98 5 H 13353 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.390 Extract box with map and model: 15.660 Check model and map are aligned: 0.390 Process input model: 90.130 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.240 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 13420 Z= 0.271 Angle : 0.763 18.480 18203 Z= 0.371 Chirality : 0.039 0.168 2092 Planarity : 0.006 0.082 2256 Dihedral : 14.908 87.355 4836 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1660 helix: 1.17 (0.16), residues: 1017 sheet: -1.66 (0.49), residues: 114 loop : -1.84 (0.25), residues: 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.5623 time to fit residues: 224.3990 Evaluate side-chains 223 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 GLN A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13420 Z= 0.297 Angle : 0.578 11.724 18203 Z= 0.301 Chirality : 0.039 0.128 2092 Planarity : 0.005 0.081 2256 Dihedral : 8.564 89.988 1830 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1660 helix: 1.18 (0.16), residues: 1013 sheet: -1.84 (0.49), residues: 114 loop : -1.91 (0.25), residues: 533 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 221 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 230 average time/residue: 0.5475 time to fit residues: 188.8845 Evaluate side-chains 221 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3245 time to fit residues: 9.8744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 13420 Z= 0.262 Angle : 0.561 12.025 18203 Z= 0.290 Chirality : 0.039 0.155 2092 Planarity : 0.005 0.081 2256 Dihedral : 8.124 87.650 1830 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1660 helix: 1.18 (0.16), residues: 1011 sheet: -1.70 (0.51), residues: 108 loop : -1.96 (0.25), residues: 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 224 average time/residue: 0.5391 time to fit residues: 179.8299 Evaluate side-chains 214 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 2.073 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2925 time to fit residues: 5.0137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 151 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13420 Z= 0.272 Angle : 0.562 11.540 18203 Z= 0.292 Chirality : 0.039 0.203 2092 Planarity : 0.005 0.080 2256 Dihedral : 7.685 84.164 1830 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1660 helix: 1.12 (0.16), residues: 1011 sheet: -1.85 (0.50), residues: 110 loop : -1.96 (0.25), residues: 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 225 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 232 average time/residue: 0.5524 time to fit residues: 190.1684 Evaluate side-chains 227 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 215 time to evaluate : 2.106 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3243 time to fit residues: 9.5542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13420 Z= 0.223 Angle : 0.546 11.328 18203 Z= 0.281 Chirality : 0.038 0.130 2092 Planarity : 0.005 0.080 2256 Dihedral : 7.214 79.904 1830 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1660 helix: 1.21 (0.16), residues: 1010 sheet: -1.71 (0.51), residues: 108 loop : -1.94 (0.25), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 227 average time/residue: 0.5718 time to fit residues: 193.1978 Evaluate side-chains 220 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 217 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3233 time to fit residues: 4.5073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13420 Z= 0.225 Angle : 0.543 11.260 18203 Z= 0.279 Chirality : 0.038 0.201 2092 Planarity : 0.005 0.080 2256 Dihedral : 6.627 73.654 1830 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1660 helix: 1.24 (0.16), residues: 1008 sheet: -1.78 (0.50), residues: 110 loop : -1.90 (0.25), residues: 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 225 average time/residue: 0.6183 time to fit residues: 211.0336 Evaluate side-chains 224 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 2.160 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3260 time to fit residues: 8.0163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 772 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 13420 Z= 0.169 Angle : 0.522 10.992 18203 Z= 0.265 Chirality : 0.038 0.152 2092 Planarity : 0.005 0.081 2256 Dihedral : 5.907 63.604 1830 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1660 helix: 1.38 (0.16), residues: 1010 sheet: -1.53 (0.52), residues: 106 loop : -1.87 (0.25), residues: 544 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 224 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 225 average time/residue: 0.5282 time to fit residues: 177.5202 Evaluate side-chains 222 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2956 time to fit residues: 3.7743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 13420 Z= 0.238 Angle : 0.545 11.344 18203 Z= 0.280 Chirality : 0.038 0.196 2092 Planarity : 0.005 0.081 2256 Dihedral : 5.514 62.445 1830 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1660 helix: 1.31 (0.16), residues: 1010 sheet: -1.61 (0.52), residues: 106 loop : -1.87 (0.25), residues: 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 220 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 223 average time/residue: 0.5566 time to fit residues: 186.3749 Evaluate side-chains 227 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 2.266 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3289 time to fit residues: 7.5760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 13420 Z= 0.189 Angle : 0.530 11.104 18203 Z= 0.270 Chirality : 0.038 0.193 2092 Planarity : 0.005 0.081 2256 Dihedral : 5.081 61.889 1830 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1660 helix: 1.38 (0.16), residues: 1009 sheet: -1.56 (0.52), residues: 106 loop : -1.82 (0.25), residues: 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 225 average time/residue: 0.6021 time to fit residues: 204.5963 Evaluate side-chains 221 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 2.186 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3405 time to fit residues: 3.9121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13420 Z= 0.169 Angle : 0.522 11.026 18203 Z= 0.265 Chirality : 0.038 0.186 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.705 61.548 1830 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1660 helix: 1.45 (0.16), residues: 1012 sheet: -1.52 (0.53), residues: 106 loop : -1.79 (0.26), residues: 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 566 is missing expected H atoms. Skipping. Residue ALA 566 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 226 average time/residue: 0.5700 time to fit residues: 191.8514 Evaluate side-chains 223 residues out of total 1403 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4102 time to fit residues: 5.5203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126490 restraints weight = 56137.672| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.35 r_work: 0.3431 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13420 Z= 0.204 Angle : 0.536 11.241 18203 Z= 0.274 Chirality : 0.038 0.168 2092 Planarity : 0.005 0.081 2256 Dihedral : 4.635 60.855 1830 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1660 helix: 1.40 (0.16), residues: 1011 sheet: -1.53 (0.53), residues: 106 loop : -1.79 (0.26), residues: 543 =============================================================================== Job complete usr+sys time: 6119.20 seconds wall clock time: 110 minutes 6.62 seconds (6606.62 seconds total)