Starting phenix.real_space_refine on Tue Dec 31 06:42:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dde_46771/12_2024/9dde_46771.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dde_46771/12_2024/9dde_46771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dde_46771/12_2024/9dde_46771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dde_46771/12_2024/9dde_46771.map" model { file = "/net/cci-nas-00/data/ceres_data/9dde_46771/12_2024/9dde_46771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dde_46771/12_2024/9dde_46771.cif" } resolution = 3.2 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= 0.006 sd= 0.059 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 324 5.49 5 S 34 5.16 5 C 8654 2.51 5 N 2852 2.21 5 O 3525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15394 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3345 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3297 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "K" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 783 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 93} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 467 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "O" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 467 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12728 SG CYS K 18 110.369 47.497 86.380 1.00172.81 S ATOM 12749 SG CYS K 21 113.957 46.507 85.515 1.00171.27 S ATOM 12887 SG CYS K 39 112.069 48.574 83.128 1.00170.07 S ATOM 12909 SG CYS K 42 111.045 44.883 83.675 1.00170.96 S ATOM 12846 SG CYS K 34 98.527 51.073 90.704 1.00173.73 S ATOM 12996 SG CYS K 53 100.863 48.206 91.830 1.00177.96 S ATOM 13017 SG CYS K 56 98.621 49.902 94.368 1.00184.67 S ATOM 13653 SG CYS L 51 100.265 74.273 84.400 1.00185.19 S ATOM 13674 SG CYS L 54 101.442 77.195 86.194 1.00181.49 S ATOM 13815 SG CYS L 72 100.667 73.995 88.092 1.00169.07 S ATOM 13834 SG CYS L 75 97.777 76.217 86.748 1.00168.71 S ATOM 13769 SG CYS L 67 94.926 63.191 78.331 1.00151.96 S ATOM 13923 SG CYS L 87 95.103 66.989 77.587 1.00170.12 S ATOM 13943 SG CYS L 90 95.202 64.478 74.680 1.00157.27 S ATOM 14193 SG CYS M 27 29.418 51.535 66.943 1.00123.52 S ATOM 14212 SG CYS M 30 27.721 52.692 63.677 1.00112.94 S ATOM 14292 SG CYS M 41 29.720 49.538 63.755 1.00100.03 S ATOM 14312 SG CYS M 44 31.513 52.805 63.995 1.00 94.27 S Time building chain proxies: 9.55, per 1000 atoms: 0.62 Number of scatterers: 15394 At special positions: 0 Unit cell: (137.541, 124.545, 144.039, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 34 16.00 P 324 15.00 O 3525 8.00 N 2852 7.00 C 8654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 24 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 16 sheets defined 60.5% alpha, 5.8% beta 161 base pairs and 290 stacking pairs defined. Time for finding SS restraints: 7.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.503A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.892A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.645A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.175A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.632A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.502A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 14 through 16 No H-bonds generated for 'chain 'K' and resid 14 through 16' Processing helix chain 'K' and resid 40 through 48 Processing helix chain 'K' and resid 64 through 67 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 73 through 83 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 103 through 114 Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'O' and resid 38 through 51 removed outlier: 4.345A pdb=" N LEU O 42 " --> pdb=" O PRO O 38 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS O 51 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 69 Processing helix chain 'O' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.482A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.852A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.861A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.295A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AB4, first strand: chain 'L' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB6, first strand: chain 'N' and resid 12 through 16 removed outlier: 9.330A pdb=" N LEU N 67 " --> pdb=" O GLN N 2 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU N 69 " --> pdb=" O PHE N 4 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 56 through 57 523 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 415 hydrogen bonds 830 hydrogen bond angles 0 basepair planarities 161 basepair parallelities 290 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3440 1.33 - 1.46: 4869 1.46 - 1.58: 7316 1.58 - 1.70: 646 1.70 - 1.82: 46 Bond restraints: 16317 Sorted by residual: bond pdb=" N GLY M 49 " pdb=" CA GLY M 49 " ideal model delta sigma weight residual 1.444 1.477 -0.033 9.60e-03 1.09e+04 1.18e+01 bond pdb=" N ASN K 13 " pdb=" CA ASN K 13 " ideal model delta sigma weight residual 1.462 1.494 -0.032 9.50e-03 1.11e+04 1.15e+01 bond pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.08e-02 8.57e+03 9.51e+00 bond pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.95e+00 bond pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 1.462 1.487 -0.026 9.50e-03 1.11e+04 7.36e+00 ... (remaining 16312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 22940 1.91 - 3.81: 484 3.81 - 5.72: 42 5.72 - 7.63: 15 7.63 - 9.54: 1 Bond angle restraints: 23482 Sorted by residual: angle pdb=" CB LYS K 81 " pdb=" CG LYS K 81 " pdb=" CD LYS K 81 " ideal model delta sigma weight residual 111.30 120.84 -9.54 2.30e+00 1.89e-01 1.72e+01 angle pdb=" N ASN B 25 " pdb=" CA ASN B 25 " pdb=" C ASN B 25 " ideal model delta sigma weight residual 114.12 108.81 5.31 1.39e+00 5.18e-01 1.46e+01 angle pdb=" N ASP G 72 " pdb=" CA ASP G 72 " pdb=" C ASP G 72 " ideal model delta sigma weight residual 112.54 108.51 4.03 1.22e+00 6.72e-01 1.09e+01 angle pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" C ASN F 25 " ideal model delta sigma weight residual 113.23 109.20 4.03 1.24e+00 6.50e-01 1.06e+01 angle pdb=" CA ASP B 24 " pdb=" C ASP B 24 " pdb=" O ASP B 24 " ideal model delta sigma weight residual 122.03 118.12 3.91 1.25e+00 6.40e-01 9.81e+00 ... (remaining 23477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.75: 6847 26.75 - 53.50: 1840 53.50 - 80.25: 274 80.25 - 107.00: 3 107.00 - 133.76: 2 Dihedral angle restraints: 8966 sinusoidal: 5630 harmonic: 3336 Sorted by residual: dihedral pdb=" C4' DC I 36 " pdb=" C3' DC I 36 " pdb=" O3' DC I 36 " pdb=" P DT I 37 " ideal model delta sinusoidal sigma weight residual 220.00 86.24 133.76 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" CA LYS K 8 " pdb=" C LYS K 8 " pdb=" N ILE K 9 " pdb=" CA ILE K 9 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" C4' DC I 128 " pdb=" C3' DC I 128 " pdb=" O3' DC I 128 " pdb=" P DT I 129 " ideal model delta sinusoidal sigma weight residual 220.00 91.73 128.27 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 8963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2694 0.109 - 0.218: 27 0.218 - 0.326: 1 0.326 - 0.435: 0 0.435 - 0.544: 6 Chirality restraints: 2728 Sorted by residual: chirality pdb=" P DC I 173 " pdb=" OP1 DC I 173 " pdb=" OP2 DC I 173 " pdb=" O5' DC I 173 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" P DA J 151 " pdb=" OP1 DA J 151 " pdb=" OP2 DA J 151 " pdb=" O5' DA J 151 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" P DG I 174 " pdb=" OP1 DG I 174 " pdb=" OP2 DG I 174 " pdb=" O5' DG I 174 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 2725 not shown) Planarity restraints: 1851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 48 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C ASP D 48 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP D 48 " -0.018 2.00e-02 2.50e+03 pdb=" N THR D 49 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.019 2.00e-02 2.50e+03 1.61e-02 5.16e+00 pdb=" CG TYR D 80 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " 0.193 9.50e-02 1.11e+02 8.64e-02 4.59e+00 pdb=" NE ARG B 23 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " 0.007 2.00e-02 2.50e+03 ... (remaining 1848 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2156 2.76 - 3.30: 13224 3.30 - 3.83: 28260 3.83 - 4.37: 32748 4.37 - 4.90: 48324 Nonbonded interactions: 124712 Sorted by model distance: nonbonded pdb=" OE2 GLU O 52 " pdb=" OG SER O 54 " model vdw 2.226 3.040 nonbonded pdb=" N GLN L 25 " pdb=" OE1 GLN L 25 " model vdw 2.229 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.239 3.040 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.248 3.120 nonbonded pdb=" O LEU L 80 " pdb=" NZ LYS L 85 " model vdw 2.297 3.120 ... (remaining 124707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.660 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16317 Z= 0.247 Angle : 0.649 9.537 23482 Z= 0.394 Chirality : 0.044 0.544 2728 Planarity : 0.005 0.086 1851 Dihedral : 26.365 133.756 6802 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.33 % Allowed : 14.32 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.25), residues: 1121 helix: 2.48 (0.20), residues: 658 sheet: 0.20 (0.85), residues: 35 loop : -0.86 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 25 HIS 0.009 0.001 HIS C 31 PHE 0.013 0.001 PHE E 78 TYR 0.038 0.002 TYR D 80 ARG 0.009 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8917 (tttp) cc_final: 0.8701 (ttmm) REVERT: F 67 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8132 (ttm-80) REVERT: K 70 ARG cc_start: 0.8713 (mmt90) cc_final: 0.8464 (mmt-90) REVERT: K 74 THR cc_start: 0.8779 (p) cc_final: 0.8491 (t) REVERT: K 80 TYR cc_start: 0.8022 (m-80) cc_final: 0.7786 (m-10) REVERT: K 90 GLU cc_start: 0.9083 (tp30) cc_final: 0.8862 (tp30) REVERT: L 61 THR cc_start: 0.9312 (m) cc_final: 0.9015 (p) REVERT: L 71 PHE cc_start: 0.8741 (m-80) cc_final: 0.8198 (m-80) REVERT: M 61 LEU cc_start: 0.7939 (tp) cc_final: 0.7280 (pt) outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.3561 time to fit residues: 148.6377 Evaluate side-chains 247 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 0.0050 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS H 46 HIS K 76 GLN N 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 16317 Z= 0.433 Angle : 0.645 9.786 23482 Z= 0.379 Chirality : 0.040 0.141 2728 Planarity : 0.005 0.048 1851 Dihedral : 28.975 122.611 4782 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.89 % Allowed : 17.20 % Favored : 79.91 % 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: 1.80 (0.25), residues: 1121 helix: 2.49 (0.20), residues: 662 sheet: 0.09 (0.88), residues: 35 loop : -0.87 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 17 HIS 0.004 0.001 HIS C 31 PHE 0.017 0.002 PHE M 24 TYR 0.056 0.002 TYR D 80 ARG 0.007 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8721 (mtt180) REVERT: H 73 GLU cc_start: 0.8399 (tp30) cc_final: 0.7823 (tp30) REVERT: K 70 ARG cc_start: 0.9084 (mmt90) cc_final: 0.8441 (mmt-90) REVERT: K 74 THR cc_start: 0.8971 (p) cc_final: 0.8750 (t) REVERT: L 61 THR cc_start: 0.9280 (m) cc_final: 0.8927 (p) REVERT: L 78 THR cc_start: 0.9384 (m) cc_final: 0.9167 (p) REVERT: M 61 LEU cc_start: 0.8573 (tp) cc_final: 0.8183 (pt) REVERT: O 105 LYS cc_start: 0.8837 (ptpt) cc_final: 0.8249 (ptpt) outliers start: 26 outliers final: 18 residues processed: 254 average time/residue: 0.3332 time to fit residues: 116.3308 Evaluate side-chains 245 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain N residue 8 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16317 Z= 0.234 Angle : 0.566 8.323 23482 Z= 0.336 Chirality : 0.035 0.147 2728 Planarity : 0.004 0.039 1851 Dihedral : 28.702 120.293 4782 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.22 % Allowed : 18.09 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.05 (0.25), residues: 1121 helix: 2.73 (0.20), residues: 660 sheet: 0.13 (0.88), residues: 35 loop : -0.82 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 25 HIS 0.002 0.001 HIS F 75 PHE 0.014 0.001 PHE E 78 TYR 0.015 0.001 TYR D 80 ARG 0.005 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8008 (tp30) cc_final: 0.7778 (tp30) REVERT: G 17 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8608 (mtt180) REVERT: K 70 ARG cc_start: 0.9041 (mmt90) cc_final: 0.8425 (mmt-90) REVERT: K 74 THR cc_start: 0.8979 (p) cc_final: 0.8649 (t) REVERT: L 71 PHE cc_start: 0.8614 (m-80) cc_final: 0.8265 (m-80) REVERT: L 78 THR cc_start: 0.9392 (m) cc_final: 0.9187 (p) REVERT: L 92 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8736 (mtmm) REVERT: M 61 LEU cc_start: 0.8648 (tp) cc_final: 0.8326 (pt) REVERT: O 105 LYS cc_start: 0.8816 (ptpt) cc_final: 0.8282 (ptpt) outliers start: 20 outliers final: 16 residues processed: 252 average time/residue: 0.3364 time to fit residues: 117.4370 Evaluate side-chains 244 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0040 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 75 HIS C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16317 Z= 0.207 Angle : 0.553 8.083 23482 Z= 0.329 Chirality : 0.034 0.140 2728 Planarity : 0.004 0.040 1851 Dihedral : 28.537 120.185 4782 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.78 % Allowed : 19.87 % Favored : 78.36 % 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: 2.08 (0.25), residues: 1121 helix: 2.72 (0.20), residues: 666 sheet: -0.18 (0.87), residues: 35 loop : -0.77 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP M 25 HIS 0.005 0.001 HIS L 69 PHE 0.016 0.001 PHE K 38 TYR 0.017 0.001 TYR D 80 ARG 0.006 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8045 (tp30) cc_final: 0.7760 (tp30) REVERT: K 27 ASP cc_start: 0.8316 (p0) cc_final: 0.7981 (p0) REVERT: K 40 LYS cc_start: 0.9322 (ttmt) cc_final: 0.9068 (ptmt) REVERT: K 70 ARG cc_start: 0.9053 (mmt90) cc_final: 0.8450 (mmt-90) REVERT: K 74 THR cc_start: 0.9006 (p) cc_final: 0.8672 (t) REVERT: L 71 PHE cc_start: 0.8622 (m-80) cc_final: 0.8332 (m-80) REVERT: L 78 THR cc_start: 0.9403 (m) cc_final: 0.9192 (p) REVERT: L 92 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8755 (mtmm) REVERT: M 61 LEU cc_start: 0.8711 (tp) cc_final: 0.8411 (pt) REVERT: O 105 LYS cc_start: 0.8724 (ptpt) cc_final: 0.8252 (ptpt) outliers start: 16 outliers final: 13 residues processed: 248 average time/residue: 0.3159 time to fit residues: 109.4129 Evaluate side-chains 245 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN K 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16317 Z= 0.254 Angle : 0.567 8.817 23482 Z= 0.335 Chirality : 0.035 0.149 2728 Planarity : 0.004 0.036 1851 Dihedral : 28.647 121.631 4782 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.89 % Allowed : 19.20 % Favored : 77.91 % 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: 2.09 (0.26), residues: 1121 helix: 2.67 (0.20), residues: 670 sheet: -0.13 (0.91), residues: 35 loop : -0.68 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP M 25 HIS 0.003 0.001 HIS L 69 PHE 0.014 0.001 PHE K 38 TYR 0.015 0.001 TYR D 80 ARG 0.006 0.000 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8079 (tp30) cc_final: 0.7729 (tp30) REVERT: G 17 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8688 (mtt180) REVERT: K 27 ASP cc_start: 0.8258 (p0) cc_final: 0.7876 (p0) REVERT: K 40 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8976 (ptmt) REVERT: K 46 TYR cc_start: 0.9264 (t80) cc_final: 0.8828 (t80) REVERT: K 59 GLN cc_start: 0.9276 (tt0) cc_final: 0.8926 (tm-30) REVERT: K 60 VAL cc_start: 0.8343 (t) cc_final: 0.7786 (p) REVERT: K 70 ARG cc_start: 0.9025 (mmt90) cc_final: 0.8407 (mmt-90) REVERT: K 74 THR cc_start: 0.9020 (p) cc_final: 0.8695 (t) REVERT: L 71 PHE cc_start: 0.8547 (m-80) cc_final: 0.8290 (m-80) REVERT: L 78 THR cc_start: 0.9432 (m) cc_final: 0.9230 (p) REVERT: L 92 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8798 (mtmm) REVERT: L 106 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9187 (m-80) REVERT: M 61 LEU cc_start: 0.8781 (tp) cc_final: 0.8499 (pt) REVERT: O 105 LYS cc_start: 0.8679 (ptpt) cc_final: 0.8190 (ptpt) outliers start: 26 outliers final: 19 residues processed: 250 average time/residue: 0.3301 time to fit residues: 114.3562 Evaluate side-chains 252 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 106 PHE Chi-restraints excluded: chain M residue 27 CYS Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.9222 > 50: distance: 36 - 37: 7.287 distance: 36 - 41: 3.822 distance: 37 - 145: 7.160 distance: 38 - 39: 8.313 distance: 38 - 40: 6.859 distance: 47 - 48: 3.126 distance: 48 - 51: 5.547 distance: 49 - 50: 4.225 distance: 49 - 55: 5.284 distance: 50 - 73: 30.641 distance: 51 - 52: 9.947 distance: 52 - 53: 10.836 distance: 52 - 54: 12.456 distance: 56 - 57: 5.867 distance: 56 - 59: 10.206 distance: 57 - 58: 5.349 distance: 57 - 60: 3.335 distance: 58 - 82: 40.995 distance: 60 - 61: 10.552 distance: 61 - 62: 8.192 distance: 61 - 64: 6.068 distance: 62 - 63: 5.782 distance: 62 - 65: 4.406 distance: 63 - 87: 22.888 distance: 65 - 66: 4.388 distance: 66 - 67: 14.176 distance: 66 - 69: 11.546 distance: 67 - 68: 10.286 distance: 67 - 73: 14.702 distance: 68 - 92: 24.491 distance: 69 - 70: 6.402 distance: 70 - 71: 4.622 distance: 70 - 72: 8.086 distance: 73 - 74: 12.230 distance: 74 - 75: 15.466 distance: 74 - 77: 5.466 distance: 75 - 76: 19.713 distance: 75 - 82: 28.479 distance: 76 - 100: 24.413 distance: 77 - 78: 4.978 distance: 78 - 79: 5.282 distance: 79 - 80: 10.164 distance: 80 - 81: 3.664 distance: 82 - 83: 30.587 distance: 83 - 84: 10.578 distance: 83 - 86: 26.327 distance: 84 - 85: 10.061 distance: 84 - 87: 10.018 distance: 85 - 105: 21.493 distance: 87 - 88: 6.508 distance: 88 - 89: 5.364 distance: 88 - 91: 3.111 distance: 89 - 90: 4.512 distance: 89 - 92: 4.898 distance: 90 - 110: 9.663 distance: 92 - 93: 5.069 distance: 93 - 94: 4.423 distance: 93 - 96: 7.839 distance: 95 - 115: 3.113 distance: 96 - 97: 13.200 distance: 97 - 98: 13.580 distance: 97 - 99: 5.771