Starting phenix.real_space_refine on Mon Nov 20 12:35:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajb_15476/11_2023/8ajb_15476.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajb_15476/11_2023/8ajb_15476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajb_15476/11_2023/8ajb_15476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajb_15476/11_2023/8ajb_15476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajb_15476/11_2023/8ajb_15476.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ajb_15476/11_2023/8ajb_15476.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 18156 2.51 5 N 5852 2.21 5 O 6012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "E ARG 839": "NH1" <-> "NH2" Residue "E ARG 873": "NH1" <-> "NH2" Residue "F ARG 808": "NH1" <-> "NH2" Residue "F ARG 818": "NH1" <-> "NH2" Residue "F ARG 839": "NH1" <-> "NH2" Residue "F ARG 873": "NH1" <-> "NH2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "I GLU 340": "OE1" <-> "OE2" Residue "I GLU 375": "OE1" <-> "OE2" Residue "I GLU 397": "OE1" <-> "OE2" Residue "I GLU 410": "OE1" <-> "OE2" Residue "J GLU 397": "OE1" <-> "OE2" Residue "J GLU 431": "OE1" <-> "OE2" Residue "K ARG 808": "NH1" <-> "NH2" Residue "K ARG 839": "NH1" <-> "NH2" Residue "K ARG 873": "NH1" <-> "NH2" Residue "L ARG 808": "NH1" <-> "NH2" Residue "L ARG 818": "NH1" <-> "NH2" Residue "L ARG 839": "NH1" <-> "NH2" Residue "L ARG 873": "NH1" <-> "NH2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M GLU 137": "OE1" <-> "OE2" Residue "M GLU 142": "OE1" <-> "OE2" Residue "M GLU 196": "OE1" <-> "OE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N GLU 78": "OE1" <-> "OE2" Residue "N GLU 108": "OE1" <-> "OE2" Residue "N GLU 137": "OE1" <-> "OE2" Residue "N GLU 172": "OE1" <-> "OE2" Residue "N GLU 212": "OE1" <-> "OE2" Residue "O GLU 234": "OE1" <-> "OE2" Residue "O GLU 288": "OE1" <-> "OE2" Residue "O GLU 340": "OE1" <-> "OE2" Residue "O GLU 375": "OE1" <-> "OE2" Residue "O GLU 382": "OE1" <-> "OE2" Residue "O GLU 431": "OE1" <-> "OE2" Residue "P GLU 330": "OE1" <-> "OE2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "Q ARG 808": "NH1" <-> "NH2" Residue "Q ARG 839": "NH1" <-> "NH2" Residue "Q ARG 873": "NH1" <-> "NH2" Residue "R ARG 808": "NH1" <-> "NH2" Residue "R ARG 818": "NH1" <-> "NH2" Residue "R ARG 839": "NH1" <-> "NH2" Residue "R ARG 873": "NH1" <-> "NH2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S GLU 110": "OE1" <-> "OE2" Residue "S GLU 137": "OE1" <-> "OE2" Residue "T GLU 78": "OE1" <-> "OE2" Residue "U GLU 340": "OE1" <-> "OE2" Residue "U GLU 375": "OE1" <-> "OE2" Residue "U GLU 397": "OE1" <-> "OE2" Residue "U GLU 410": "OE1" <-> "OE2" Residue "V GLU 397": "OE1" <-> "OE2" Residue "V GLU 431": "OE1" <-> "OE2" Residue "W ARG 808": "NH1" <-> "NH2" Residue "W ARG 839": "NH1" <-> "NH2" Residue "W ARG 873": "NH1" <-> "NH2" Residue "X ARG 808": "NH1" <-> "NH2" Residue "X ARG 818": "NH1" <-> "NH2" Residue "X ARG 839": "NH1" <-> "NH2" Residue "X ARG 873": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 30088 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 2, 'TRANS': 242} Chain: "B" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1828 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 2, 'TRANS': 235} Chain: "C" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "D" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "F" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1203 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "H" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1264 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "J" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 820 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 2, 'TRANS': 242} Chain: "N" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1828 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 2, 'TRANS': 235} Chain: "O" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "P" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1793 Classifications: {'peptide': 234} Link IDs: {'TRANS': 233} Chain: "Q" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "R" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "S" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1203 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "T" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1264 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain: "U" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "V" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "W" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "X" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 820 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Time building chain proxies: 15.21, per 1000 atoms: 0.51 Number of scatterers: 30088 At special positions: 0 Unit cell: (151.05, 570.81, 90.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 6012 8.00 N 5852 7.00 C 18156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 795 " - pdb=" SG CYS E 868 " distance=2.03 Simple disulfide: pdb=" SG CYS F 795 " - pdb=" SG CYS F 868 " distance=2.06 Simple disulfide: pdb=" SG CYS K 795 " - pdb=" SG CYS K 868 " distance=2.03 Simple disulfide: pdb=" SG CYS L 795 " - pdb=" SG CYS L 868 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 795 " - pdb=" SG CYS Q 868 " distance=2.03 Simple disulfide: pdb=" SG CYS R 795 " - pdb=" SG CYS R 868 " distance=2.06 Simple disulfide: pdb=" SG CYS W 795 " - pdb=" SG CYS W 868 " distance=2.03 Simple disulfide: pdb=" SG CYS X 795 " - pdb=" SG CYS X 868 " 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: 14.72 Conformation dependent library (CDL) restraints added in 7.0 seconds 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7360 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 22 sheets defined 78.2% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 35 through 61 removed outlier: 3.937A pdb=" N ALA A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 70 through 83 removed outlier: 4.468A pdb=" N ARG A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 277 Processing helix chain 'B' and resid 41 through 277 Proline residue: B 64 - end of helix Proline residue: B 72 - end of helix removed outlier: 3.987A pdb=" N ARG B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 446 removed outlier: 4.258A pdb=" N ARG C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 446 Processing helix chain 'E' and resid 859 through 863 Processing helix chain 'F' and resid 859 through 863 Processing helix chain 'G' and resid 40 through 193 Proline residue: G 64 - end of helix Proline residue: G 72 - end of helix removed outlier: 4.018A pdb=" N ALA G 92 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 193 Proline residue: H 64 - end of helix Proline residue: H 72 - end of helix removed outlier: 4.104A pdb=" N ALA H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL H 90 " --> pdb=" O GLU H 86 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG H 91 " --> pdb=" O LEU H 87 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 446 removed outlier: 3.687A pdb=" N GLY I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL I 353 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR I 355 " --> pdb=" O ALA I 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 446 Processing helix chain 'K' and resid 833 through 837 removed outlier: 3.580A pdb=" N LYS K 837 " --> pdb=" O ASP K 834 " (cutoff:3.500A) Processing helix chain 'K' and resid 859 through 863 Processing helix chain 'L' and resid 859 through 863 Processing helix chain 'M' and resid 35 through 61 removed outlier: 3.938A pdb=" N ALA M 61 " --> pdb=" O GLU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 69 Processing helix chain 'M' and resid 70 through 83 removed outlier: 4.467A pdb=" N ARG M 81 " --> pdb=" O PHE M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 277 Processing helix chain 'N' and resid 41 through 277 Proline residue: N 64 - end of helix Proline residue: N 72 - end of helix removed outlier: 3.987A pdb=" N ARG N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 446 removed outlier: 4.258A pdb=" N ARG O 357 " --> pdb=" O VAL O 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 214 through 446 Processing helix chain 'Q' and resid 859 through 863 Processing helix chain 'R' and resid 859 through 863 Processing helix chain 'S' and resid 40 through 193 Proline residue: S 64 - end of helix Proline residue: S 72 - end of helix removed outlier: 4.019A pdb=" N ALA S 92 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 193 Proline residue: T 64 - end of helix Proline residue: T 72 - end of helix removed outlier: 4.104A pdb=" N ALA T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL T 90 " --> pdb=" O GLU T 86 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG T 91 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA T 92 " --> pdb=" O ILE T 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 446 removed outlier: 3.687A pdb=" N GLY U 352 " --> pdb=" O GLN U 348 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL U 353 " --> pdb=" O ARG U 349 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR U 355 " --> pdb=" O ALA U 351 " (cutoff:3.500A) Processing helix chain 'V' and resid 328 through 446 Processing helix chain 'W' and resid 833 through 837 removed outlier: 3.581A pdb=" N LYS W 837 " --> pdb=" O ASP W 834 " (cutoff:3.500A) Processing helix chain 'W' and resid 859 through 863 Processing helix chain 'X' and resid 859 through 863 Processing sheet with id=AA1, first strand: chain 'E' and resid 791 through 793 removed outlier: 4.132A pdb=" N ASP E 845 " --> pdb=" O THR E 850 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 830 through 832 removed outlier: 3.572A pdb=" N ASN E 831 " --> pdb=" O VAL E 823 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP E 809 " --> pdb=" O VAL E 821 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL E 823 " --> pdb=" O MET E 807 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET E 807 " --> pdb=" O VAL E 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 869 through 872 removed outlier: 3.773A pdb=" N ALA E 870 " --> pdb=" O TYR E 877 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.916A pdb=" N GLN F 5 " --> pdb=" O ALA F 796 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER F 794 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 820 through 824 removed outlier: 5.030A pdb=" N MET F 820 " --> pdb=" O ARG F 811 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG F 811 " --> pdb=" O MET F 820 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 822 " --> pdb=" O TRP F 809 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 842 through 845 Processing sheet with id=AA7, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.995A pdb=" N CYS K 795 " --> pdb=" O VAL K 851 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL K 851 " --> pdb=" O CYS K 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 818 through 824 removed outlier: 6.977A pdb=" N TRP K 809 " --> pdb=" O VAL K 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL K 823 " --> pdb=" O MET K 807 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET K 807 " --> pdb=" O VAL K 823 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE K 806 " --> pdb=" O ILE K 871 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 818 through 824 removed outlier: 6.977A pdb=" N TRP K 809 " --> pdb=" O VAL K 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL K 823 " --> pdb=" O MET K 807 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET K 807 " --> pdb=" O VAL K 823 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE K 806 " --> pdb=" O ILE K 871 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA K 864 " --> pdb=" O VAL K 884 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL K 884 " --> pdb=" O ALA K 864 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.862A pdb=" N THR L 850 " --> pdb=" O ASP L 845 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP L 845 " --> pdb=" O THR L 850 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE L 841 " --> pdb=" O GLN L 854 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 830 through 832 removed outlier: 6.570A pdb=" N TRP L 809 " --> pdb=" O VAL L 821 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL L 823 " --> pdb=" O MET L 807 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N MET L 807 " --> pdb=" O VAL L 823 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 791 through 793 removed outlier: 4.133A pdb=" N ASP Q 845 " --> pdb=" O THR Q 850 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 830 through 832 removed outlier: 3.571A pdb=" N ASN Q 831 " --> pdb=" O VAL Q 823 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TRP Q 809 " --> pdb=" O VAL Q 821 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL Q 823 " --> pdb=" O MET Q 807 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET Q 807 " --> pdb=" O VAL Q 823 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 869 through 872 removed outlier: 3.772A pdb=" N ALA Q 870 " --> pdb=" O TYR Q 877 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.916A pdb=" N GLN R 5 " --> pdb=" O ALA R 796 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER R 794 " --> pdb=" O SER R 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 820 through 824 removed outlier: 5.030A pdb=" N MET R 820 " --> pdb=" O ARG R 811 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG R 811 " --> pdb=" O MET R 820 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA R 822 " --> pdb=" O TRP R 809 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 842 through 845 Processing sheet with id=AB9, first strand: chain 'W' and resid 4 through 5 removed outlier: 3.995A pdb=" N CYS W 795 " --> pdb=" O VAL W 851 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL W 851 " --> pdb=" O CYS W 795 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 818 through 824 removed outlier: 6.976A pdb=" N TRP W 809 " --> pdb=" O VAL W 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL W 823 " --> pdb=" O MET W 807 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET W 807 " --> pdb=" O VAL W 823 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE W 806 " --> pdb=" O ILE W 871 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 818 through 824 removed outlier: 6.976A pdb=" N TRP W 809 " --> pdb=" O VAL W 821 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL W 823 " --> pdb=" O MET W 807 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET W 807 " --> pdb=" O VAL W 823 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE W 806 " --> pdb=" O ILE W 871 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA W 864 " --> pdb=" O VAL W 884 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL W 884 " --> pdb=" O ALA W 864 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 5 through 6 removed outlier: 3.863A pdb=" N THR X 850 " --> pdb=" O ASP X 845 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP X 845 " --> pdb=" O THR X 850 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE X 841 " --> pdb=" O GLN X 854 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 830 through 832 removed outlier: 6.569A pdb=" N TRP X 809 " --> pdb=" O VAL X 821 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL X 823 " --> pdb=" O MET X 807 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N MET X 807 " --> pdb=" O VAL X 823 " (cutoff:3.500A) 3044 hydrogen bonds defined for protein. 9000 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: 10.73 Time building geometry restraints manager: 15.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11132 1.34 - 1.46: 5670 1.46 - 1.59: 13348 1.59 - 1.72: 0 1.72 - 1.84: 120 Bond restraints: 30270 Sorted by residual: bond pdb=" N ILE K 804 " pdb=" CA ILE K 804 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.99e+00 bond pdb=" N ILE W 804 " pdb=" CA ILE W 804 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.85e+00 bond pdb=" N ARG I 349 " pdb=" CA ARG I 349 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.34e+00 bond pdb=" N HIS I 350 " pdb=" CA HIS I 350 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.30e+00 bond pdb=" N HIS U 350 " pdb=" CA HIS U 350 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.28e-02 6.10e+03 6.26e+00 ... (remaining 30265 not shown) Histogram of bond angle deviations from ideal: 95.77 - 103.46: 101 103.46 - 111.16: 11673 111.16 - 118.86: 13283 118.86 - 126.55: 15498 126.55 - 134.25: 171 Bond angle restraints: 40726 Sorted by residual: angle pdb=" C TYR H 42 " pdb=" N GLU H 43 " pdb=" CA GLU H 43 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" C TYR T 42 " pdb=" N GLU T 43 " pdb=" CA GLU T 43 " ideal model delta sigma weight residual 120.28 112.64 7.64 1.34e+00 5.57e-01 3.25e+01 angle pdb=" N THR R 885 " pdb=" CA THR R 885 " pdb=" C THR R 885 " ideal model delta sigma weight residual 108.07 115.90 -7.83 1.38e+00 5.25e-01 3.22e+01 angle pdb=" N THR F 885 " pdb=" CA THR F 885 " pdb=" C THR F 885 " ideal model delta sigma weight residual 108.07 115.88 -7.81 1.38e+00 5.25e-01 3.20e+01 angle pdb=" CA GLU B 76 " pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " ideal model delta sigma weight residual 114.10 103.53 10.57 2.00e+00 2.50e-01 2.79e+01 ... (remaining 40721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16808 17.95 - 35.89: 1820 35.89 - 53.84: 252 53.84 - 71.78: 78 71.78 - 89.73: 64 Dihedral angle restraints: 19022 sinusoidal: 7734 harmonic: 11288 Sorted by residual: dihedral pdb=" CB CYS R 795 " pdb=" SG CYS R 795 " pdb=" SG CYS R 868 " pdb=" CB CYS R 868 " ideal model delta sinusoidal sigma weight residual -86.00 -32.68 -53.32 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS F 795 " pdb=" SG CYS F 795 " pdb=" SG CYS F 868 " pdb=" CB CYS F 868 " ideal model delta sinusoidal sigma weight residual -86.00 -32.71 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA ARG H 80 " pdb=" C ARG H 80 " pdb=" N ARG H 81 " pdb=" CA ARG H 81 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 19019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4002 0.074 - 0.149: 565 0.149 - 0.223: 62 0.223 - 0.298: 11 0.298 - 0.372: 6 Chirality restraints: 4646 Sorted by residual: chirality pdb=" CB VAL A 73 " pdb=" CA VAL A 73 " pdb=" CG1 VAL A 73 " pdb=" CG2 VAL A 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB VAL M 73 " pdb=" CA VAL M 73 " pdb=" CG1 VAL M 73 " pdb=" CG2 VAL M 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA GLU B 76 " pdb=" N GLU B 76 " pdb=" C GLU B 76 " pdb=" CB GLU B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 4643 not shown) Planarity restraints: 5518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA X 813 " -0.057 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO X 814 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO X 814 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO X 814 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 813 " 0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO L 814 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO L 814 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO L 814 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 809 " -0.037 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP R 809 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 809 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP R 809 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP R 809 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 809 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 809 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 809 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 809 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 809 " -0.022 2.00e-02 2.50e+03 ... (remaining 5515 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 32 2.16 - 2.84: 10370 2.84 - 3.53: 53280 3.53 - 4.21: 69025 4.21 - 4.90: 117291 Nonbonded interactions: 249998 Sorted by model distance: nonbonded pdb=" NE2 GLN D 396 " pdb=" CZ ARG Q 873 " model vdw 1.475 3.350 nonbonded pdb=" NE2 GLN D 396 " pdb=" NH1 ARG Q 873 " model vdw 1.596 3.200 nonbonded pdb=" CZ ARG E 873 " pdb=" NE2 GLN P 396 " model vdw 1.604 3.350 nonbonded pdb=" NH1 ARG E 873 " pdb=" NE2 GLN P 396 " model vdw 1.643 3.200 nonbonded pdb=" CB ILE K 804 " pdb=" CE1 TYR K 872 " model vdw 1.847 3.770 ... (remaining 249993 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 40 through 277) selection = chain 'B' selection = (chain 'M' and resid 40 through 277) selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'O' selection = chain 'P' } ncs_group { reference = (chain 'E' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'F' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'K' and (resid 1 through 8 or resid 791 through 887)) selection = chain 'L' selection = (chain 'Q' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'R' and (resid 1 through 8 or resid 791 through 887)) selection = (chain 'W' and (resid 1 through 8 or resid 791 through 887)) selection = chain 'X' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 39 through 193) selection = chain 'S' selection = (chain 'T' and resid 39 through 193) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 16.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 45.950 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 82.160 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 30270 Z= 0.425 Angle : 1.034 15.759 40726 Z= 0.590 Chirality : 0.053 0.372 4646 Planarity : 0.005 0.085 5518 Dihedral : 15.630 89.725 11638 Min Nonbonded Distance : 1.475 Molprobity Statistics. All-atom Clashscore : 32.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.13), residues: 3834 helix: 1.42 (0.09), residues: 2898 sheet: -2.73 (0.27), residues: 302 loop : -1.82 (0.24), residues: 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1136 time to evaluate : 3.610 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1136 average time/residue: 0.5344 time to fit residues: 883.6584 Evaluate side-chains 930 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 930 time to evaluate : 3.433 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 0.9990 chunk 289 optimal weight: 0.0870 chunk 160 optimal weight: 0.6980 chunk 98 optimal weight: 0.0670 chunk 195 optimal weight: 0.3980 chunk 154 optimal weight: 0.5980 chunk 299 optimal weight: 0.2980 chunk 115 optimal weight: 0.2980 chunk 182 optimal weight: 0.9980 chunk 222 optimal weight: 0.1980 chunk 346 optimal weight: 0.0970 overall best weight: 0.1494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN C 249 GLN ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN D 303 GLN ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN G 139 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 GLN I 386 GLN J 374 GLN K 805 ASN K 817 GLN L 856 ASN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 GLN M 272 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN ** O 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 GLN R 812 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 854 GLN ** S 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 386 GLN U 445 GLN V 374 GLN ** W 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 817 GLN W 856 ASN X 812 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5360 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30270 Z= 0.221 Angle : 0.708 12.787 40726 Z= 0.372 Chirality : 0.041 0.243 4646 Planarity : 0.005 0.056 5518 Dihedral : 4.804 29.594 4368 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.66 % Allowed : 7.55 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.13), residues: 3834 helix: 2.68 (0.09), residues: 2880 sheet: -2.30 (0.26), residues: 306 loop : -1.43 (0.23), residues: 648 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1032 time to evaluate : 3.330 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 1044 average time/residue: 0.5117 time to fit residues: 786.4846 Evaluate side-chains 901 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 893 time to evaluate : 3.359 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3161 time to fit residues: 9.6162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 0.2980 chunk 107 optimal weight: 0.2980 chunk 288 optimal weight: 0.6980 chunk 236 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 347 optimal weight: 0.9990 chunk 375 optimal weight: 0.9990 chunk 309 optimal weight: 0.9990 chunk 344 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 278 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 817 GLN K 831 ASN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 ASN N 98 GLN ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 GLN O 253 ASN ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 396 GLN O 417 GLN P 409 HIS R 817 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 HIS ** S 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 ASN ** T 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 401 GLN ** W 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 817 GLN W 854 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30270 Z= 0.330 Angle : 0.775 14.367 40726 Z= 0.411 Chirality : 0.044 0.328 4646 Planarity : 0.005 0.071 5518 Dihedral : 4.884 29.727 4368 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.40 % Allowed : 6.99 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.13), residues: 3834 helix: 2.61 (0.09), residues: 2892 sheet: -2.07 (0.26), residues: 374 loop : -1.32 (0.25), residues: 568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 986 time to evaluate : 3.632 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 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 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: 12 outliers final: 5 residues processed: 992 average time/residue: 0.5153 time to fit residues: 757.4400 Evaluate side-chains 890 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 885 time to evaluate : 3.426 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2911 time to fit residues: 7.4780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 0.3980 chunk 261 optimal weight: 0.9980 chunk 180 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 165 optimal weight: 0.2980 chunk 233 optimal weight: 0.7980 chunk 348 optimal weight: 0.9980 chunk 369 optimal weight: 0.0970 chunk 182 optimal weight: 0.4980 chunk 330 optimal weight: 0.2980 chunk 99 optimal weight: 0.0970 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 100 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN D 326 ASN F 856 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 GLN K 817 GLN K 831 ASN L 854 GLN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 ASN M 249 GLN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 817 GLN ** R 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 817 GLN ** R 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 374 GLN W 805 ASN W 856 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30270 Z= 0.238 Angle : 0.702 15.452 40726 Z= 0.370 Chirality : 0.042 0.293 4646 Planarity : 0.005 0.058 5518 Dihedral : 4.611 30.760 4368 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.40 % Allowed : 4.22 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.13), residues: 3834 helix: 2.97 (0.09), residues: 2870 sheet: -1.91 (0.27), residues: 334 loop : -1.27 (0.23), residues: 630 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 982 time to evaluate : 3.823 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 989 average time/residue: 0.5148 time to fit residues: 753.6842 Evaluate side-chains 898 residues out of total 3032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 892 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3031 time to fit residues: 7.9630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.1128 > 50: distance: 19 - 113: 12.233 distance: 22 - 110: 21.028 distance: 63 - 118: 26.426 distance: 72 - 101: 32.257 distance: 75 - 98: 35.159 distance: 93 - 98: 33.934 distance: 98 - 99: 20.250 distance: 99 - 100: 33.024 distance: 99 - 102: 56.565 distance: 100 - 101: 17.073 distance: 100 - 110: 16.085 distance: 102 - 103: 37.084 distance: 103 - 104: 20.623 distance: 103 - 105: 20.656 distance: 104 - 106: 8.719 distance: 105 - 107: 14.012 distance: 106 - 108: 17.271 distance: 107 - 108: 16.304 distance: 108 - 109: 22.200 distance: 110 - 111: 16.863 distance: 111 - 112: 39.095 distance: 111 - 114: 20.869 distance: 112 - 113: 34.859 distance: 112 - 118: 38.324 distance: 114 - 115: 33.069 distance: 115 - 116: 23.214 distance: 115 - 117: 41.534 distance: 118 - 119: 16.156 distance: 119 - 120: 48.668 distance: 119 - 122: 54.581 distance: 120 - 121: 42.302 distance: 120 - 127: 49.315 distance: 122 - 123: 64.693 distance: 123 - 124: 66.516 distance: 124 - 125: 33.121 distance: 124 - 126: 51.358 distance: 127 - 128: 21.247 distance: 128 - 129: 4.239 distance: 128 - 131: 18.027 distance: 129 - 130: 18.300 distance: 129 - 135: 42.596 distance: 131 - 132: 53.242 distance: 132 - 133: 56.189 distance: 133 - 134: 33.440 distance: 135 - 136: 27.502 distance: 136 - 137: 22.843 distance: 136 - 139: 10.741 distance: 137 - 138: 29.054 distance: 137 - 143: 39.605 distance: 139 - 140: 55.618 distance: 140 - 141: 17.406 distance: 140 - 142: 57.541 distance: 143 - 144: 39.208 distance: 144 - 147: 39.679 distance: 145 - 146: 40.857 distance: 145 - 151: 40.409 distance: 147 - 148: 39.392 distance: 148 - 149: 49.040 distance: 148 - 150: 28.592 distance: 151 - 152: 13.197 distance: 152 - 153: 38.036 distance: 152 - 155: 47.728 distance: 153 - 154: 61.259 distance: 153 - 159: 34.532 distance: 155 - 156: 48.545 distance: 156 - 157: 10.405 distance: 156 - 158: 37.720 distance: 159 - 160: 7.733 distance: 160 - 161: 39.078 distance: 160 - 163: 53.039 distance: 161 - 162: 56.894 distance: 161 - 168: 17.577 distance: 162 - 184: 34.408 distance: 163 - 164: 36.861 distance: 164 - 165: 19.860 distance: 165 - 166: 13.586 distance: 166 - 167: 24.358 distance: 168 - 169: 21.912 distance: 168 - 174: 45.433 distance: 169 - 170: 21.910 distance: 169 - 172: 21.699 distance: 170 - 171: 40.812 distance: 170 - 175: 18.485 distance: 171 - 192: 27.593 distance: 172 - 173: 40.036 distance: 173 - 174: 39.349 distance: 175 - 176: 44.283 distance: 176 - 177: 39.429 distance: 176 - 179: 40.020 distance: 177 - 178: 40.494 distance: 177 - 184: 31.553 distance: 179 - 180: 41.232 distance: 180 - 181: 55.896 distance: 181 - 182: 40.343 distance: 181 - 183: 25.124