Starting phenix.real_space_refine (version: dev) on Thu Feb 23 05:45:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/02_2023/7tnm_26014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/02_2023/7tnm_26014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/02_2023/7tnm_26014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/02_2023/7tnm_26014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/02_2023/7tnm_26014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/02_2023/7tnm_26014_updated.pdb" } resolution = 4.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1203": "NH1" <-> "NH2" 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: 19448 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.81, per 1000 atoms: 0.56 Number of scatterers: 19448 At special positions: 0 Unit cell: (122.01, 117.03, 135.29, 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) Cl 4 17.00 S 136 16.00 O 3594 8.00 N 3144 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.34 Conformation dependent library (CDL) restraints added in 2.9 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 20 sheets defined 50.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 523 through 544 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 624 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 758 through 769 Processing helix chain 'A' and resid 793 through 819 Processing helix chain 'A' and resid 1005 through 1027 Processing helix chain 'A' and resid 1092 through 1102 Processing helix chain 'A' and resid 1105 through 1122 Processing helix chain 'A' and resid 1133 through 1160 Processing helix chain 'A' and resid 1177 through 1208 Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.715A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 519 Processing helix chain 'B' and resid 523 through 544 Processing helix chain 'B' and resid 564 through 567 No H-bonds generated for 'chain 'B' and resid 564 through 567' Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 616 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 776 through 779 No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 790 through 818 removed outlier: 5.738A pdb=" N GLY B 794 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 798 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 804 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 805 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 809 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 813 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 817 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1028 Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1092 through 1102 Processing helix chain 'B' and resid 1105 through 1124 Processing helix chain 'B' and resid 1133 through 1160 removed outlier: 4.542A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 516 through 519 Processing helix chain 'C' and resid 523 through 544 Processing helix chain 'C' and resid 565 through 568 No H-bonds generated for 'chain 'C' and resid 565 through 568' Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 624 Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 755 Processing helix chain 'C' and resid 758 through 769 Processing helix chain 'C' and resid 793 through 819 Processing helix chain 'C' and resid 1005 through 1027 Processing helix chain 'C' and resid 1092 through 1102 Processing helix chain 'C' and resid 1105 through 1122 Processing helix chain 'C' and resid 1133 through 1160 Processing helix chain 'C' and resid 1177 through 1208 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.714A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 519 Processing helix chain 'D' and resid 523 through 544 Processing helix chain 'D' and resid 564 through 567 No H-bonds generated for 'chain 'D' and resid 564 through 567' Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 616 Processing helix chain 'D' and resid 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 755 Processing helix chain 'D' and resid 758 through 768 removed outlier: 3.501A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 779 No H-bonds generated for 'chain 'D' and resid 776 through 779' Processing helix chain 'D' and resid 790 through 818 removed outlier: 5.738A pdb=" N GLY D 794 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 798 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 804 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 805 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 809 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 813 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 817 " --> pdb=" O PHE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1028 Processing helix chain 'D' and resid 1040 through 1042 No H-bonds generated for 'chain 'D' and resid 1040 through 1042' Processing helix chain 'D' and resid 1092 through 1102 Processing helix chain 'D' and resid 1105 through 1124 Processing helix chain 'D' and resid 1133 through 1160 removed outlier: 4.542A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.613A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1033 through 1035 Processing sheet with id= E, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.698A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.046A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.592A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1033 through 1037 Processing sheet with id= J, first strand: chain 'B' and resid 1064 through 1066 Processing sheet with id= K, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= L, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= M, first strand: chain 'C' and resid 702 through 705 removed outlier: 3.612A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1033 through 1035 Processing sheet with id= O, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.698A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= Q, first strand: chain 'D' and resid 496 through 499 removed outlier: 4.046A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.592A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 1033 through 1037 Processing sheet with id= T, first strand: chain 'D' and resid 1064 through 1066 945 hydrogen bonds defined for protein. 2667 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: 6.24 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5439 1.34 - 1.46: 4181 1.46 - 1.58: 10034 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19882 Sorted by residual: bond pdb=" N THR D1049 " pdb=" CA THR D1049 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 6.99e+00 bond pdb=" N THR B1049 " pdb=" CA THR B1049 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.95e+00 bond pdb=" N LYS D1052 " pdb=" CA LYS D1052 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.15e-02 7.56e+03 5.73e+00 bond pdb=" N LYS B1052 " pdb=" CA LYS B1052 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.63e+00 bond pdb=" N SER B1050 " pdb=" CA SER B1050 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.61e+00 ... (remaining 19877 not shown) Histogram of bond angle deviations from ideal: 93.28 - 101.54: 88 101.54 - 109.80: 2825 109.80 - 118.07: 12179 118.07 - 126.33: 11458 126.33 - 134.59: 314 Bond angle restraints: 26864 Sorted by residual: angle pdb=" C ARG A1130 " pdb=" N HIS A1131 " pdb=" CA HIS A1131 " ideal model delta sigma weight residual 121.54 131.98 -10.44 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C ARG C1130 " pdb=" N HIS C1131 " pdb=" CA HIS C1131 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C LYS A1051 " pdb=" N LYS A1052 " pdb=" CA LYS A1052 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C LYS C1051 " pdb=" N LYS C1052 " pdb=" CA LYS C1052 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C GLY D1161 " pdb=" N ASP D1162 " pdb=" CA ASP D1162 " ideal model delta sigma weight residual 123.10 128.13 -5.03 9.60e-01 1.09e+00 2.74e+01 ... (remaining 26859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.08: 11184 20.08 - 40.15: 441 40.15 - 60.23: 67 60.23 - 80.30: 8 80.30 - 100.38: 6 Dihedral angle restraints: 11706 sinusoidal: 4574 harmonic: 7132 Sorted by residual: dihedral pdb=" CA PRO D1083 " pdb=" C PRO D1083 " pdb=" N GLU D1084 " pdb=" CA GLU D1084 " ideal model delta harmonic sigma weight residual 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO B1083 " pdb=" C PRO B1083 " pdb=" N GLU B1084 " pdb=" CA GLU B1084 " ideal model delta harmonic sigma weight residual 180.00 127.11 52.89 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 175.81 -82.81 1 1.00e+01 1.00e-02 8.40e+01 ... (remaining 11703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2619 0.082 - 0.164: 324 0.164 - 0.246: 36 0.246 - 0.328: 13 0.328 - 0.410: 6 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU C1002 " pdb=" CB LEU C1002 " pdb=" CD1 LEU C1002 " pdb=" CD2 LEU C1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CG LEU A1002 " pdb=" CB LEU A1002 " pdb=" CD1 LEU A1002 " pdb=" CD2 LEU A1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2995 not shown) Planarity restraints: 3314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 513 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLY B 513 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY B 513 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 514 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 513 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLY D 513 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY D 513 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL D 514 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 421 " 0.032 2.00e-02 2.50e+03 1.70e-02 5.76e+00 pdb=" CG TYR A 421 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 421 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 421 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 421 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 421 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 421 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 421 " 0.023 2.00e-02 2.50e+03 ... (remaining 3311 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2064 2.75 - 3.29: 20484 3.29 - 3.83: 32725 3.83 - 4.36: 37955 4.36 - 4.90: 63575 Nonbonded interactions: 156803 Sorted by model distance: nonbonded pdb=" O PHE D1106 " pdb=" OG SER D1147 " model vdw 2.214 2.440 nonbonded pdb=" O PHE B1106 " pdb=" OG SER B1147 " model vdw 2.214 2.440 nonbonded pdb=" O PHE C1106 " pdb=" OG SER C1147 " model vdw 2.252 2.440 nonbonded pdb=" O PHE A1106 " pdb=" OG SER A1147 " model vdw 2.253 2.440 nonbonded pdb=" O PRO C1107 " pdb=" OG SER C1110 " model vdw 2.295 2.440 ... (remaining 156798 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 394 through 819 or resid 1002 through 1209 or resid 1302)) \ selection = (chain 'B' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) selection = (chain 'C' and (resid 394 through 819 or resid 1002 through 1209 or resid 1302)) \ selection = (chain 'D' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) } 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12570 2.51 5 N 3144 2.21 5 O 3594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.010 Extract box with map and model: 8.210 Check model and map are aligned: 0.300 Process input model: 50.560 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 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 : 0.007 0.075 19882 Z= 0.430 Angle : 1.075 13.326 26864 Z= 0.587 Chirality : 0.060 0.410 2998 Planarity : 0.006 0.049 3314 Dihedral : 11.182 100.379 7122 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.56 % Favored : 96.95 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 2460 helix: -0.43 (0.11), residues: 1318 sheet: -0.85 (0.37), residues: 150 loop : -1.65 (0.17), residues: 992 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 744 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 755 average time/residue: 0.3169 time to fit residues: 358.0483 Evaluate side-chains 392 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 2.345 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1586 time to fit residues: 3.6392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 chunk 225 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 619 ASN A1204 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN B 791 ASN B1081 HIS B1171 ASN C 569 ASN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C1081 HIS C1204 HIS ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN D1081 HIS D1171 ASN D1198 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19882 Z= 0.204 Angle : 0.637 7.465 26864 Z= 0.340 Chirality : 0.042 0.168 2998 Planarity : 0.005 0.046 3314 Dihedral : 6.710 90.926 2694 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.46 % Favored : 96.22 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 (0.16), residues: 2460 helix: 1.33 (0.13), residues: 1330 sheet: -0.72 (0.37), residues: 150 loop : -1.25 (0.19), residues: 980 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 540 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 546 average time/residue: 0.2778 time to fit residues: 240.0014 Evaluate side-chains 347 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 344 time to evaluate : 2.415 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1847 time to fit residues: 4.2595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 243 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 19882 Z= 0.209 Angle : 0.616 7.643 26864 Z= 0.324 Chirality : 0.042 0.174 2998 Planarity : 0.004 0.052 3314 Dihedral : 6.450 89.850 2694 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.89 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.40 (0.16), residues: 2460 helix: 1.55 (0.14), residues: 1318 sheet: -1.16 (0.35), residues: 164 loop : -1.29 (0.19), residues: 978 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 474 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 478 average time/residue: 0.2754 time to fit residues: 210.7437 Evaluate side-chains 333 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 330 time to evaluate : 2.326 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1879 time to fit residues: 4.1812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 226 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19882 Z= 0.219 Angle : 0.610 6.773 26864 Z= 0.322 Chirality : 0.042 0.165 2998 Planarity : 0.004 0.053 3314 Dihedral : 6.247 90.211 2694 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.04 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.36 (0.17), residues: 2460 helix: 1.48 (0.14), residues: 1332 sheet: -1.35 (0.37), residues: 144 loop : -1.25 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 440 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 441 average time/residue: 0.2754 time to fit residues: 194.3331 Evaluate side-chains 320 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 HIS B1008 GLN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19882 Z= 0.203 Angle : 0.602 7.890 26864 Z= 0.315 Chirality : 0.041 0.186 2998 Planarity : 0.004 0.054 3314 Dihedral : 6.192 92.447 2694 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.36 (0.17), residues: 2460 helix: 1.50 (0.14), residues: 1332 sheet: -1.62 (0.37), residues: 142 loop : -1.26 (0.19), residues: 986 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 437 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.2679 time to fit residues: 189.6276 Evaluate side-chains 310 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B1008 GLN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1148 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN D 747 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 19882 Z= 0.253 Angle : 0.633 8.448 26864 Z= 0.333 Chirality : 0.042 0.228 2998 Planarity : 0.004 0.064 3314 Dihedral : 6.226 93.546 2694 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.28 (0.17), residues: 2460 helix: 1.44 (0.14), residues: 1322 sheet: -1.66 (0.38), residues: 146 loop : -1.26 (0.19), residues: 992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.223 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: 0 outliers final: 0 residues processed: 415 average time/residue: 0.2664 time to fit residues: 179.0878 Evaluate side-chains 288 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 110 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: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 HIS B1008 GLN ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1148 ASN C1159 ASN C1204 HIS ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 19882 Z= 0.203 Angle : 0.607 7.399 26864 Z= 0.315 Chirality : 0.041 0.189 2998 Planarity : 0.004 0.074 3314 Dihedral : 6.118 92.728 2694 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.39 (0.17), residues: 2460 helix: 1.50 (0.14), residues: 1326 sheet: -1.46 (0.36), residues: 160 loop : -1.18 (0.20), residues: 974 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2707 time to fit residues: 183.2896 Evaluate side-chains 301 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN B1131 HIS ** C 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19882 Z= 0.177 Angle : 0.602 8.999 26864 Z= 0.309 Chirality : 0.041 0.188 2998 Planarity : 0.004 0.064 3314 Dihedral : 5.977 93.056 2694 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2460 helix: 1.54 (0.14), residues: 1328 sheet: -1.56 (0.36), residues: 168 loop : -1.12 (0.20), residues: 964 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.2688 time to fit residues: 179.6394 Evaluate side-chains 306 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 5.9990 chunk 208 optimal weight: 0.0770 chunk 222 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 chunk 97 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 chunk 201 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN B1008 GLN B1198 HIS C 575 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 19882 Z= 0.176 Angle : 0.598 9.763 26864 Z= 0.306 Chirality : 0.041 0.217 2998 Planarity : 0.004 0.061 3314 Dihedral : 5.892 92.869 2694 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2460 helix: 1.56 (0.14), residues: 1320 sheet: -1.53 (0.35), residues: 174 loop : -1.13 (0.20), residues: 966 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.2687 time to fit residues: 181.0679 Evaluate side-chains 304 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 247 optimal weight: 0.0060 chunk 227 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 151 optimal weight: 0.2980 chunk 120 optimal weight: 0.0970 chunk 156 optimal weight: 7.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 19882 Z= 0.181 Angle : 0.605 11.120 26864 Z= 0.309 Chirality : 0.041 0.194 2998 Planarity : 0.004 0.060 3314 Dihedral : 5.841 92.974 2694 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2460 helix: 1.55 (0.14), residues: 1318 sheet: -1.56 (0.35), residues: 176 loop : -1.12 (0.20), residues: 966 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2666 time to fit residues: 175.4909 Evaluate side-chains 306 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.089439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.069314 restraints weight = 88568.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071373 restraints weight = 60270.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072863 restraints weight = 45154.362| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.6098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 19882 Z= 0.196 Angle : 0.619 9.018 26864 Z= 0.318 Chirality : 0.042 0.231 2998 Planarity : 0.004 0.060 3314 Dihedral : 5.841 93.239 2694 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.42 (0.17), residues: 2460 helix: 1.53 (0.14), residues: 1320 sheet: -1.32 (0.36), residues: 168 loop : -1.18 (0.20), residues: 972 =============================================================================== Job complete usr+sys time: 4226.29 seconds wall clock time: 77 minutes 38.99 seconds (4658.99 seconds total)