Starting phenix.real_space_refine on Thu Jun 12 03:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqk_34028/06_2025/7yqk_34028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqk_34028/06_2025/7yqk_34028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqk_34028/06_2025/7yqk_34028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqk_34028/06_2025/7yqk_34028.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqk_34028/06_2025/7yqk_34028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqk_34028/06_2025/7yqk_34028.cif" } resolution = 3.38 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 20 5.16 5 C 7742 2.51 5 N 2559 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13745 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 745 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, '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: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "O" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "K" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 140 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 948 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 115} Time building chain proxies: 8.13, per 1000 atoms: 0.59 Number of scatterers: 13745 At special positions: 0 Unit cell: (115.56, 107, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 288 15.00 O 3136 8.00 N 2559 7.00 C 7742 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: 3.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 56.6% alpha, 7.3% beta 132 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.809A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.611A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.575A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.658A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.486A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.720A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.580A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.930A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.612A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.724A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.550A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.600A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.974A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.625A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.703A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.372A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.792A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 4.016A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.599A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.575A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.088A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 32 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'N' and resid 1528 through 1530 No H-bonds generated for 'chain 'N' and resid 1528 through 1530' Processing helix chain 'N' and resid 1589 through 1594 Processing helix chain 'N' and resid 1596 through 1601 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.971A 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 96 through 98 removed outlier: 6.384A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.640A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.037A 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 'G' and resid 42 through 43 removed outlier: 7.210A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'O' and resid 13 through 15 removed outlier: 3.524A pdb=" N ILE O 3 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 1502 through 1503 Processing sheet with id=AB3, first strand: chain 'N' and resid 1506 through 1509 removed outlier: 6.913A pdb=" N ILE N1506 " --> pdb=" O LEU N1518 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU N1518 " --> pdb=" O ILE N1506 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG N1508 " --> pdb=" O LYS N1516 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU N1517 " --> pdb=" O CYS N1525 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS N1525 " --> pdb=" O LEU N1517 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 1577 through 1582 removed outlier: 5.899A pdb=" N GLU N1567 " --> pdb=" O LYS N1563 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS N1563 " --> pdb=" O GLU N1567 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR N1569 " --> pdb=" O HIS N1561 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS N1561 " --> pdb=" O TYR N1569 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER N1571 " --> pdb=" O LYS N1559 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER N1554 " --> pdb=" O ALA N1546 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 662 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 6.71 Time building geometry restraints manager: 4.21 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: 3236 1.33 - 1.45: 4265 1.45 - 1.57: 6465 1.57 - 1.69: 576 1.69 - 1.81: 32 Bond restraints: 14574 Sorted by residual: bond pdb=" CG1 ILE B 66 " pdb=" CD1 ILE B 66 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CG LEU F 62 " pdb=" CD2 LEU F 62 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C ILE A 119 " pdb=" N MET A 120 " ideal model delta sigma weight residual 1.325 1.310 0.015 1.25e-02 6.40e+03 1.52e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 14569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 20186 1.61 - 3.22: 654 3.22 - 4.84: 52 4.84 - 6.45: 14 6.45 - 8.06: 4 Bond angle restraints: 20910 Sorted by residual: angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.39 117.13 -6.74 1.75e+00 3.27e-01 1.48e+01 angle pdb=" C LEU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 121.18 114.67 6.51 1.98e+00 2.55e-01 1.08e+01 angle pdb=" C ILE A 124 " pdb=" N GLN A 125 " pdb=" CA GLN A 125 " ideal model delta sigma weight residual 121.58 115.37 6.21 1.95e+00 2.63e-01 1.02e+01 angle pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.87e+00 angle pdb=" C TYR O 59 " pdb=" N ASN O 60 " pdb=" CA ASN O 60 " ideal model delta sigma weight residual 122.46 126.37 -3.91 1.41e+00 5.03e-01 7.69e+00 ... (remaining 20905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 6498 31.42 - 62.83: 1499 62.83 - 94.25: 34 94.25 - 125.66: 1 125.66 - 157.08: 2 Dihedral angle restraints: 8034 sinusoidal: 5188 harmonic: 2846 Sorted by residual: dihedral pdb=" CA ASP K1616 " pdb=" C ASP K1616 " pdb=" N ILE K1617 " pdb=" CA ILE K1617 " ideal model delta harmonic sigma weight residual -180.00 -142.46 -37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA SER K1618 " pdb=" C SER K1618 " pdb=" N LEU K1619 " pdb=" CA LEU K1619 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LYS G 13 " pdb=" C LYS G 13 " pdb=" N ALA G 14 " pdb=" CA ALA G 14 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1538 0.032 - 0.064: 631 0.064 - 0.096: 141 0.096 - 0.128: 53 0.128 - 0.160: 8 Chirality restraints: 2371 Sorted by residual: chirality pdb=" CB ILE O 36 " pdb=" CA ILE O 36 " pdb=" CG1 ILE O 36 " pdb=" CG2 ILE O 36 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA GLU B 63 " pdb=" N GLU B 63 " pdb=" C GLU B 63 " pdb=" CB GLU B 63 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 2368 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 116 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO C 117 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO G 80 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 93 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C GLN A 93 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 93 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 94 " -0.012 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 445 2.66 - 3.22: 12603 3.22 - 3.78: 25550 3.78 - 4.34: 32935 4.34 - 4.90: 46313 Nonbonded interactions: 117846 Sorted by model distance: nonbonded pdb=" N2 DG I 52 " pdb=" O2 DC J -52 " model vdw 2.105 2.496 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.130 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O LEU C 23 " model vdw 2.166 3.040 nonbonded pdb=" O HIS H 109 " pdb=" OG SER H 112 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLU A 50 " pdb=" NH1 ARG B 39 " model vdw 2.203 3.120 ... (remaining 117841 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 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 10 through 118 or (resid 119 through 120 and (name N or na \ me CA or name C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 30 through 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 124)) selection = chain 'H' } 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=0.00 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: 1.570 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.210 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14574 Z= 0.226 Angle : 0.657 8.061 20910 Z= 0.394 Chirality : 0.038 0.160 2371 Planarity : 0.004 0.063 1646 Dihedral : 26.061 157.077 6204 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.71 (0.26), residues: 965 helix: 0.29 (0.23), residues: 537 sheet: -1.25 (0.75), residues: 34 loop : -1.41 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP N1495 HIS 0.007 0.001 HIS G 31 PHE 0.023 0.002 PHE C 25 TYR 0.032 0.002 TYR F 88 ARG 0.006 0.001 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.17655 ( 743) hydrogen bonds : angle 6.41787 ( 1853) covalent geometry : bond 0.00488 (14574) covalent geometry : angle 0.65662 (20910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.8638 (p) cc_final: 0.8309 (p) REVERT: A 97 GLU cc_start: 0.8316 (mp0) cc_final: 0.7965 (mp0) REVERT: A 125 GLN cc_start: 0.9165 (pm20) cc_final: 0.8950 (pm20) REVERT: B 59 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8771 (ttmt) REVERT: B 84 MET cc_start: 0.8761 (mmt) cc_final: 0.8325 (mmt) REVERT: B 85 ASP cc_start: 0.8968 (m-30) cc_final: 0.8534 (m-30) REVERT: B 88 TYR cc_start: 0.8994 (m-80) cc_final: 0.8735 (m-80) REVERT: C 64 GLU cc_start: 0.8797 (tp30) cc_final: 0.8328 (tp30) REVERT: C 104 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8751 (mm-40) REVERT: E 64 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8663 (mmmm) REVERT: E 79 LYS cc_start: 0.8648 (tttm) cc_final: 0.8443 (ttmm) REVERT: E 80 THR cc_start: 0.9455 (m) cc_final: 0.9219 (t) REVERT: F 44 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8633 (ttmt) REVERT: F 85 ASP cc_start: 0.9108 (m-30) cc_final: 0.8868 (m-30) REVERT: G 72 ASP cc_start: 0.9093 (m-30) cc_final: 0.8777 (m-30) REVERT: H 68 ASP cc_start: 0.9011 (t0) cc_final: 0.8802 (t0) REVERT: H 83 TYR cc_start: 0.8367 (m-80) cc_final: 0.7807 (m-80) REVERT: O 62 GLN cc_start: 0.8971 (mm110) cc_final: 0.8558 (mm110) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3767 time to fit residues: 134.2841 Evaluate side-chains 223 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.036463 restraints weight = 66372.519| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.37 r_work: 0.2511 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14574 Z= 0.184 Angle : 0.606 6.666 20910 Z= 0.353 Chirality : 0.037 0.194 2371 Planarity : 0.004 0.055 1646 Dihedral : 29.541 156.125 4264 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.20 % Allowed : 10.73 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.15 (0.27), residues: 965 helix: 1.06 (0.23), residues: 556 sheet: -0.68 (0.90), residues: 24 loop : -1.28 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.001 PHE E 67 TYR 0.031 0.002 TYR H 83 ARG 0.010 0.001 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 743) hydrogen bonds : angle 3.78359 ( 1853) covalent geometry : bond 0.00408 (14574) covalent geometry : angle 0.60605 (20910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 1.718 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: A 80 THR cc_start: 0.8602 (p) cc_final: 0.8398 (p) REVERT: A 105 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: A 106 ASP cc_start: 0.8984 (m-30) cc_final: 0.8577 (m-30) REVERT: A 108 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.9161 (t0) REVERT: B 53 GLU cc_start: 0.8239 (pm20) cc_final: 0.7967 (pm20) REVERT: B 84 MET cc_start: 0.9331 (mmt) cc_final: 0.9026 (mmt) REVERT: B 85 ASP cc_start: 0.9225 (m-30) cc_final: 0.8927 (m-30) REVERT: C 56 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8656 (mm-30) REVERT: C 64 GLU cc_start: 0.9220 (tp30) cc_final: 0.8757 (tp30) REVERT: D 71 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9230 (tp30) REVERT: E 80 THR cc_start: 0.9610 (m) cc_final: 0.9359 (t) REVERT: F 85 ASP cc_start: 0.9409 (m-30) cc_final: 0.9197 (m-30) REVERT: G 41 GLU cc_start: 0.8998 (mp0) cc_final: 0.8723 (mp0) REVERT: G 72 ASP cc_start: 0.9186 (m-30) cc_final: 0.8861 (m-30) REVERT: G 92 GLU cc_start: 0.8721 (tt0) cc_final: 0.8157 (tt0) REVERT: O 40 GLN cc_start: 0.8180 (mm110) cc_final: 0.7896 (mm110) outliers start: 18 outliers final: 12 residues processed: 267 average time/residue: 0.3616 time to fit residues: 133.7392 Evaluate side-chains 240 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.054282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.035690 restraints weight = 66307.391| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.36 r_work: 0.2494 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14574 Z= 0.190 Angle : 0.600 7.201 20910 Z= 0.347 Chirality : 0.037 0.198 2371 Planarity : 0.004 0.058 1646 Dihedral : 29.584 157.326 4264 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.66 % Allowed : 13.78 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.52 (0.27), residues: 965 helix: 1.42 (0.23), residues: 556 sheet: -0.62 (0.97), residues: 24 loop : -1.22 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.011 0.001 PHE C 25 TYR 0.028 0.001 TYR B 88 ARG 0.006 0.000 ARG K1629 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 743) hydrogen bonds : angle 3.53137 ( 1853) covalent geometry : bond 0.00423 (14574) covalent geometry : angle 0.59966 (20910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: A 106 ASP cc_start: 0.9072 (m-30) cc_final: 0.8645 (m-30) REVERT: A 125 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: B 63 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8366 (mp0) REVERT: C 56 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8776 (mm-30) REVERT: D 47 GLN cc_start: 0.9572 (mm-40) cc_final: 0.9354 (mm-40) REVERT: D 71 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9141 (tp30) REVERT: D 89 ILE cc_start: 0.9110 (mt) cc_final: 0.8851 (mt) REVERT: E 79 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8504 (ttpp) REVERT: F 52 GLU cc_start: 0.9053 (mp0) cc_final: 0.8615 (pm20) REVERT: F 85 ASP cc_start: 0.9395 (m-30) cc_final: 0.9189 (m-30) REVERT: G 41 GLU cc_start: 0.9070 (mp0) cc_final: 0.8790 (mp0) REVERT: G 72 ASP cc_start: 0.9194 (m-30) cc_final: 0.8913 (m-30) REVERT: H 83 TYR cc_start: 0.8661 (m-80) cc_final: 0.8381 (m-80) REVERT: O 40 GLN cc_start: 0.8197 (mm110) cc_final: 0.7934 (mm110) REVERT: K 1626 LYS cc_start: 0.7928 (tptt) cc_final: 0.7544 (tptt) outliers start: 30 outliers final: 16 residues processed: 255 average time/residue: 0.3853 time to fit residues: 135.3430 Evaluate side-chains 248 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 112 optimal weight: 50.0000 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 112 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.052662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034115 restraints weight = 67073.930| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.32 r_work: 0.2437 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 14574 Z= 0.271 Angle : 0.636 7.380 20910 Z= 0.367 Chirality : 0.039 0.210 2371 Planarity : 0.004 0.058 1646 Dihedral : 29.840 155.262 4264 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.27 % Allowed : 15.49 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.63 (0.27), residues: 965 helix: 1.50 (0.22), residues: 558 sheet: -0.59 (0.95), residues: 24 loop : -1.17 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.008 0.002 HIS G 31 PHE 0.012 0.001 PHE E 67 TYR 0.036 0.002 TYR B 88 ARG 0.008 0.000 ARG K1629 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 743) hydrogen bonds : angle 3.62054 ( 1853) covalent geometry : bond 0.00608 (14574) covalent geometry : angle 0.63582 (20910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8819 (mm-30) REVERT: A 106 ASP cc_start: 0.9093 (m-30) cc_final: 0.8876 (m-30) REVERT: A 125 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8852 (pm20) REVERT: B 63 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: B 85 ASP cc_start: 0.9232 (m-30) cc_final: 0.8910 (m-30) REVERT: B 88 TYR cc_start: 0.9422 (m-80) cc_final: 0.9211 (m-80) REVERT: C 84 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.9044 (tt0) REVERT: D 47 GLN cc_start: 0.9576 (mm-40) cc_final: 0.9331 (mm-40) REVERT: E 79 LYS cc_start: 0.8848 (ttpp) cc_final: 0.8352 (ttpp) REVERT: E 120 MET cc_start: 0.9192 (mpp) cc_final: 0.8970 (mtm) REVERT: F 85 ASP cc_start: 0.9417 (m-30) cc_final: 0.9180 (m-30) REVERT: G 31 HIS cc_start: 0.9104 (OUTLIER) cc_final: 0.8848 (t-90) REVERT: G 64 GLU cc_start: 0.9469 (tt0) cc_final: 0.8992 (tm-30) REVERT: G 72 ASP cc_start: 0.9156 (m-30) cc_final: 0.8836 (m-30) REVERT: O 6 LYS cc_start: 0.9374 (mmmt) cc_final: 0.9094 (mmmt) REVERT: O 40 GLN cc_start: 0.8388 (mm110) cc_final: 0.8098 (mm110) REVERT: O 49 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7857 (mm-40) REVERT: O 62 GLN cc_start: 0.9218 (mm110) cc_final: 0.8929 (mm110) outliers start: 35 outliers final: 21 residues processed: 259 average time/residue: 0.5310 time to fit residues: 191.9446 Evaluate side-chains 254 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.035661 restraints weight = 66516.156| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.30 r_work: 0.2486 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14574 Z= 0.174 Angle : 0.602 8.784 20910 Z= 0.348 Chirality : 0.036 0.188 2371 Planarity : 0.004 0.059 1646 Dihedral : 29.644 156.766 4264 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.93 % Allowed : 18.41 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.70 (0.27), residues: 965 helix: 1.54 (0.22), residues: 563 sheet: -0.31 (1.01), residues: 24 loop : -1.16 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.032 0.002 TYR D 83 ARG 0.004 0.000 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 743) hydrogen bonds : angle 3.37507 ( 1853) covalent geometry : bond 0.00391 (14574) covalent geometry : angle 0.60219 (20910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8876 (mm-30) REVERT: A 105 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8511 (tm-30) REVERT: A 106 ASP cc_start: 0.9100 (m-30) cc_final: 0.8655 (m-30) REVERT: A 125 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8829 (pm20) REVERT: B 63 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: B 85 ASP cc_start: 0.9188 (m-30) cc_final: 0.8860 (m-30) REVERT: C 56 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8845 (mm-30) REVERT: C 84 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.9061 (tt0) REVERT: E 120 MET cc_start: 0.9191 (mpp) cc_final: 0.8869 (mtm) REVERT: E 125 GLN cc_start: 0.9229 (mt0) cc_final: 0.8989 (mt0) REVERT: G 41 GLU cc_start: 0.9150 (mp0) cc_final: 0.8928 (mp0) REVERT: G 72 ASP cc_start: 0.9143 (m-30) cc_final: 0.8725 (m-30) REVERT: G 73 ASN cc_start: 0.9180 (m-40) cc_final: 0.8893 (t0) REVERT: O 6 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9107 (mmmt) REVERT: O 40 GLN cc_start: 0.8310 (mm110) cc_final: 0.8029 (mm110) REVERT: O 62 GLN cc_start: 0.9192 (mm110) cc_final: 0.8849 (mm110) REVERT: K 1626 LYS cc_start: 0.8088 (tptt) cc_final: 0.7810 (tptt) outliers start: 24 outliers final: 10 residues processed: 265 average time/residue: 0.5544 time to fit residues: 204.1586 Evaluate side-chains 251 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 237 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 48 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 overall best weight: 1.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.035583 restraints weight = 67912.801| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.34 r_work: 0.2489 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14574 Z= 0.182 Angle : 0.612 7.264 20910 Z= 0.353 Chirality : 0.037 0.207 2371 Planarity : 0.004 0.058 1646 Dihedral : 29.658 157.287 4264 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.93 % Allowed : 17.80 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.68 (0.27), residues: 965 helix: 1.55 (0.22), residues: 563 sheet: 0.11 (1.17), residues: 18 loop : -1.22 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.008 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.044 0.002 TYR B 88 ARG 0.005 0.000 ARG O 42 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 743) hydrogen bonds : angle 3.34322 ( 1853) covalent geometry : bond 0.00410 (14574) covalent geometry : angle 0.61168 (20910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8947 (mm-30) REVERT: A 105 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: A 106 ASP cc_start: 0.9136 (m-30) cc_final: 0.8725 (m-30) REVERT: A 125 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8819 (pm20) REVERT: B 59 LYS cc_start: 0.9293 (ttmt) cc_final: 0.8744 (ttpp) REVERT: B 63 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8398 (mp0) REVERT: B 85 ASP cc_start: 0.9186 (m-30) cc_final: 0.8855 (m-30) REVERT: C 84 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.9063 (tt0) REVERT: D 47 GLN cc_start: 0.9544 (mm-40) cc_final: 0.9330 (mm-40) REVERT: E 120 MET cc_start: 0.9189 (mpp) cc_final: 0.8947 (mpp) REVERT: E 125 GLN cc_start: 0.9228 (mt0) cc_final: 0.8918 (mt0) REVERT: F 52 GLU cc_start: 0.8965 (mp0) cc_final: 0.8648 (pm20) REVERT: G 41 GLU cc_start: 0.9145 (mp0) cc_final: 0.8928 (mp0) REVERT: G 72 ASP cc_start: 0.9130 (m-30) cc_final: 0.8665 (m-30) REVERT: G 73 ASN cc_start: 0.9137 (m-40) cc_final: 0.8871 (t0) REVERT: O 6 LYS cc_start: 0.9464 (mmmt) cc_final: 0.9096 (mmmt) REVERT: O 62 GLN cc_start: 0.9196 (mm110) cc_final: 0.8865 (mm110) REVERT: O 67 LEU cc_start: 0.9337 (tp) cc_final: 0.9118 (tp) outliers start: 24 outliers final: 16 residues processed: 259 average time/residue: 0.3412 time to fit residues: 122.3075 Evaluate side-chains 252 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 75 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.036851 restraints weight = 67300.884| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.36 r_work: 0.2538 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14574 Z= 0.152 Angle : 0.614 9.365 20910 Z= 0.351 Chirality : 0.036 0.224 2371 Planarity : 0.004 0.058 1646 Dihedral : 29.518 158.136 4264 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.80 % Allowed : 19.02 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.63 (0.27), residues: 965 helix: 1.53 (0.22), residues: 562 sheet: -0.84 (0.91), residues: 29 loop : -1.22 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP N1580 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.041 0.002 TYR B 88 ARG 0.004 0.000 ARG O 42 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 743) hydrogen bonds : angle 3.26222 ( 1853) covalent geometry : bond 0.00338 (14574) covalent geometry : angle 0.61417 (20910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 261 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8895 (mm-30) REVERT: A 106 ASP cc_start: 0.9142 (m-30) cc_final: 0.8937 (m-30) REVERT: A 125 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8813 (pm20) REVERT: B 59 LYS cc_start: 0.9278 (ttmt) cc_final: 0.8709 (ttpp) REVERT: B 63 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: B 85 ASP cc_start: 0.9208 (m-30) cc_final: 0.8961 (m-30) REVERT: C 56 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8769 (mm-30) REVERT: C 84 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9143 (tt0) REVERT: E 120 MET cc_start: 0.9185 (mpp) cc_final: 0.8927 (mpp) REVERT: F 52 GLU cc_start: 0.8920 (mp0) cc_final: 0.8628 (pm20) REVERT: G 31 HIS cc_start: 0.9139 (OUTLIER) cc_final: 0.8735 (t-90) REVERT: G 41 GLU cc_start: 0.9143 (mp0) cc_final: 0.8922 (mp0) REVERT: G 72 ASP cc_start: 0.9159 (m-30) cc_final: 0.8750 (m-30) REVERT: G 91 GLU cc_start: 0.9314 (pm20) cc_final: 0.8908 (pm20) REVERT: H 34 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8824 (mmtm) REVERT: H 83 TYR cc_start: 0.7907 (m-80) cc_final: 0.7606 (t80) REVERT: O 6 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9120 (mmmt) REVERT: O 62 GLN cc_start: 0.9123 (mm110) cc_final: 0.8816 (mm110) REVERT: K 1626 LYS cc_start: 0.8054 (tptt) cc_final: 0.7838 (tptt) outliers start: 23 outliers final: 12 residues processed: 268 average time/residue: 0.2814 time to fit residues: 105.7513 Evaluate side-chains 259 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.054767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.036006 restraints weight = 66644.854| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.35 r_work: 0.2520 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14574 Z= 0.177 Angle : 0.641 9.566 20910 Z= 0.364 Chirality : 0.037 0.234 2371 Planarity : 0.004 0.057 1646 Dihedral : 29.598 158.124 4264 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.68 % Allowed : 20.24 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.64 (0.27), residues: 965 helix: 1.51 (0.22), residues: 562 sheet: -0.76 (0.92), residues: 29 loop : -1.17 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N1580 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.048 0.002 TYR B 88 ARG 0.011 0.000 ARG K1629 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 743) hydrogen bonds : angle 3.38757 ( 1853) covalent geometry : bond 0.00401 (14574) covalent geometry : angle 0.64056 (20910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8907 (mm-30) REVERT: A 106 ASP cc_start: 0.9105 (m-30) cc_final: 0.8796 (m-30) REVERT: A 107 THR cc_start: 0.9806 (m) cc_final: 0.9534 (p) REVERT: A 125 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8831 (pm20) REVERT: B 59 LYS cc_start: 0.9278 (ttmt) cc_final: 0.8792 (ttpp) REVERT: B 63 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: B 85 ASP cc_start: 0.9185 (m-30) cc_final: 0.8983 (m-30) REVERT: C 84 GLN cc_start: 0.9492 (OUTLIER) cc_final: 0.9107 (tt0) REVERT: E 79 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8396 (ttpp) REVERT: E 120 MET cc_start: 0.9273 (mpp) cc_final: 0.9025 (mpp) REVERT: F 52 GLU cc_start: 0.8881 (mp0) cc_final: 0.8522 (pm20) REVERT: G 41 GLU cc_start: 0.9153 (mp0) cc_final: 0.8898 (mp0) REVERT: G 72 ASP cc_start: 0.9066 (m-30) cc_final: 0.8818 (m-30) REVERT: H 105 GLU cc_start: 0.8670 (pm20) cc_final: 0.8002 (pm20) REVERT: O 6 LYS cc_start: 0.9542 (mmmt) cc_final: 0.9244 (mmmm) outliers start: 22 outliers final: 14 residues processed: 257 average time/residue: 0.2815 time to fit residues: 101.0745 Evaluate side-chains 258 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 57.3414 > 50: distance: 44 - 47: 7.714 distance: 47 - 48: 5.618 distance: 48 - 49: 11.598 distance: 48 - 51: 17.962 distance: 49 - 50: 8.212 distance: 49 - 56: 20.349 distance: 51 - 52: 20.981 distance: 52 - 53: 26.568 distance: 53 - 54: 12.563 distance: 54 - 55: 11.571 distance: 56 - 57: 14.724 distance: 57 - 58: 11.204 distance: 57 - 60: 17.535 distance: 58 - 59: 17.252 distance: 58 - 67: 16.271 distance: 60 - 61: 14.176 distance: 61 - 62: 9.390 distance: 62 - 63: 15.477 distance: 63 - 64: 11.343 distance: 64 - 65: 10.152 distance: 64 - 66: 9.271 distance: 67 - 68: 4.085 distance: 68 - 69: 35.473 distance: 68 - 71: 20.815 distance: 69 - 70: 24.076 distance: 69 - 74: 14.561 distance: 71 - 72: 18.277 distance: 71 - 73: 22.139 distance: 74 - 75: 7.235 distance: 75 - 78: 4.988 distance: 76 - 77: 4.831 distance: 76 - 81: 8.157 distance: 78 - 79: 31.921 distance: 78 - 80: 18.506 distance: 81 - 82: 13.595 distance: 82 - 83: 28.154 distance: 82 - 85: 32.374 distance: 83 - 84: 14.088 distance: 83 - 89: 28.632 distance: 85 - 86: 8.508 distance: 85 - 87: 23.413 distance: 86 - 88: 17.607 distance: 89 - 90: 11.426 distance: 90 - 91: 18.050 distance: 90 - 93: 31.417 distance: 91 - 92: 11.312 distance: 91 - 97: 17.851 distance: 93 - 94: 10.480 distance: 94 - 95: 8.414 distance: 95 - 96: 13.812 distance: 97 - 98: 28.875 distance: 97 - 103: 41.693 distance: 98 - 99: 10.505 distance: 98 - 101: 11.576 distance: 99 - 100: 12.004 distance: 99 - 104: 11.729 distance: 100 - 129: 20.395 distance: 101 - 102: 50.842 distance: 104 - 105: 9.789 distance: 105 - 106: 12.046 distance: 105 - 108: 5.452 distance: 106 - 107: 16.119 distance: 106 - 113: 11.157 distance: 107 - 138: 25.918 distance: 108 - 109: 9.785 distance: 109 - 110: 23.565 distance: 110 - 111: 13.548 distance: 111 - 112: 29.739 distance: 114 - 115: 11.689 distance: 114 - 117: 15.934 distance: 115 - 116: 11.332 distance: 115 - 121: 10.608 distance: 116 - 144: 17.649 distance: 117 - 118: 12.123 distance: 118 - 120: 6.994 distance: 121 - 122: 8.341 distance: 122 - 123: 5.317 distance: 122 - 125: 3.312 distance: 123 - 124: 5.065 distance: 123 - 129: 14.821 distance: 124 - 148: 20.505 distance: 125 - 126: 8.921 distance: 125 - 127: 19.273 distance: 126 - 128: 11.133