Starting phenix.real_space_refine on Thu Feb 15 23:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqk_34028/02_2024/7yqk_34028.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqk_34028/02_2024/7yqk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqk_34028/02_2024/7yqk_34028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqk_34028/02_2024/7yqk_34028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqk_34028/02_2024/7yqk_34028.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqk_34028/02_2024/7yqk_34028.pdb" } 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 Residue "A ASP 123": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "K ASP 1620": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.24, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.51 Conformation dependent library (CDL) restraints added in 1.9 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: 6.39 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: 5.72 Time building geometry restraints manager: 7.90 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: 98.50 - 105.59: 1372 105.59 - 112.68: 8083 112.68 - 119.77: 5116 119.77 - 126.86: 5522 126.86 - 133.95: 817 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 2.440 nonbonded pdb=" O HIS H 109 " pdb=" OG SER H 112 " model vdw 2.193 2.440 nonbonded pdb=" OE1 GLU A 50 " pdb=" NH1 ARG B 39 " model vdw 2.203 2.520 ... (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 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: 1.180 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: 4.320 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.810 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.050 ------------------------------------------------------------------------------- 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= 0.276 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.140 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: 0.2891 time to fit residues: 102.6834 Evaluate side-chains 223 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 84 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN O 2 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14574 Z= 0.223 Angle : 0.597 6.507 20910 Z= 0.348 Chirality : 0.036 0.193 2371 Planarity : 0.004 0.055 1646 Dihedral : 29.498 156.092 4264 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.44 % Allowed : 11.10 % Favored : 86.46 % 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: 0.20 (0.27), residues: 965 helix: 1.11 (0.23), residues: 556 sheet: -0.66 (0.89), residues: 24 loop : -1.26 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.007 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.029 0.001 TYR H 83 ARG 0.005 0.000 ARG H 33 *********************** 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 275 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 255 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: A 106 ASP cc_start: 0.8303 (m-30) cc_final: 0.7774 (m-30) REVERT: B 84 MET cc_start: 0.8883 (mmt) cc_final: 0.8625 (mmt) REVERT: B 85 ASP cc_start: 0.8887 (m-30) cc_final: 0.8546 (m-30) REVERT: C 64 GLU cc_start: 0.8866 (tp30) cc_final: 0.8399 (tp30) REVERT: C 104 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8775 (mm-40) REVERT: D 71 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8582 (tp30) REVERT: E 80 THR cc_start: 0.9432 (m) cc_final: 0.9171 (t) REVERT: F 31 LYS cc_start: 0.8815 (tttm) cc_final: 0.8603 (ttpp) REVERT: F 85 ASP cc_start: 0.9136 (m-30) cc_final: 0.8873 (m-30) REVERT: G 72 ASP cc_start: 0.8958 (m-30) cc_final: 0.8630 (m-30) REVERT: O 40 GLN cc_start: 0.8015 (mm110) cc_final: 0.7763 (mm110) REVERT: O 69 LEU cc_start: 0.9517 (tp) cc_final: 0.9306 (pp) REVERT: K 1626 LYS cc_start: 0.7909 (tptt) cc_final: 0.7596 (tmtt) outliers start: 20 outliers final: 13 residues processed: 262 average time/residue: 0.3036 time to fit residues: 109.6753 Evaluate side-chains 240 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 226 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 68 ASP 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 61 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 0.0980 chunk 118 optimal weight: 40.0000 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14574 Z= 0.200 Angle : 0.573 6.864 20910 Z= 0.334 Chirality : 0.036 0.185 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.508 157.710 4264 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.90 % Allowed : 13.90 % Favored : 82.20 % 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: 0.57 (0.28), residues: 965 helix: 1.48 (0.23), residues: 556 sheet: -0.74 (0.91), residues: 24 loop : -1.21 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.027 0.001 TYR B 88 ARG 0.006 0.000 ARG K1629 *********************** 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 285 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 253 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9378 (mt) cc_final: 0.9175 (mt) REVERT: A 65 LEU cc_start: 0.9626 (mt) cc_final: 0.9421 (mt) REVERT: A 97 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: A 105 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: A 125 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8763 (pm20) REVERT: B 63 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: B 85 ASP cc_start: 0.8898 (m-30) cc_final: 0.8609 (m-30) REVERT: C 36 LYS cc_start: 0.9238 (mptt) cc_final: 0.9031 (mmtm) REVERT: C 56 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8280 (mm-30) REVERT: C 104 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8830 (mm-40) REVERT: D 34 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8374 (mmtm) REVERT: D 47 GLN cc_start: 0.9377 (mm-40) cc_final: 0.9114 (mm-40) REVERT: E 79 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8062 (ttpp) REVERT: E 106 ASP cc_start: 0.8847 (m-30) cc_final: 0.8554 (m-30) REVERT: F 31 LYS cc_start: 0.8865 (tttm) cc_final: 0.8612 (ttpp) REVERT: F 52 GLU cc_start: 0.8746 (mp0) cc_final: 0.8505 (mp0) REVERT: F 85 ASP cc_start: 0.9139 (m-30) cc_final: 0.8884 (m-30) REVERT: G 72 ASP cc_start: 0.8919 (m-30) cc_final: 0.8614 (m-30) REVERT: H 83 TYR cc_start: 0.8301 (m-80) cc_final: 0.7974 (m-80) REVERT: O 40 GLN cc_start: 0.7986 (mm110) cc_final: 0.7734 (mm110) outliers start: 32 outliers final: 22 residues processed: 262 average time/residue: 0.2810 time to fit residues: 103.1639 Evaluate side-chains 254 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 GLU 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 40 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 ASP 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 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL 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 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 108 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14574 Z= 0.206 Angle : 0.576 7.648 20910 Z= 0.334 Chirality : 0.036 0.177 2371 Planarity : 0.004 0.057 1646 Dihedral : 29.548 158.315 4264 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.78 % Allowed : 15.85 % Favored : 80.37 % 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 (0.28), residues: 965 helix: 1.58 (0.23), residues: 562 sheet: -0.67 (0.92), residues: 24 loop : -1.19 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.005 0.001 HIS G 31 PHE 0.009 0.001 PHE E 67 TYR 0.031 0.001 TYR B 88 ARG 0.006 0.000 ARG D 79 *********************** 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 279 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 248 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: A 106 ASP cc_start: 0.8368 (m-30) cc_final: 0.8033 (m-30) REVERT: A 125 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8708 (pm20) REVERT: A 133 GLU cc_start: 0.7983 (mp0) cc_final: 0.7743 (pm20) REVERT: B 59 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8532 (ttpp) REVERT: B 63 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: B 85 ASP cc_start: 0.8928 (m-30) cc_final: 0.8552 (m-30) REVERT: C 36 LYS cc_start: 0.9247 (mptt) cc_final: 0.9031 (mmtm) REVERT: C 56 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8185 (mm-30) REVERT: C 68 ASN cc_start: 0.9169 (m-40) cc_final: 0.8855 (m-40) REVERT: C 84 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: C 104 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8792 (mm-40) REVERT: E 79 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8292 (ttpp) REVERT: E 125 GLN cc_start: 0.9098 (mt0) cc_final: 0.8829 (mt0) REVERT: F 31 LYS cc_start: 0.8869 (tttm) cc_final: 0.8596 (ttpp) REVERT: F 52 GLU cc_start: 0.8741 (mp0) cc_final: 0.8473 (mp0) REVERT: F 85 ASP cc_start: 0.9107 (m-30) cc_final: 0.8839 (m-30) REVERT: G 72 ASP cc_start: 0.8916 (m-30) cc_final: 0.8468 (m-30) REVERT: G 73 ASN cc_start: 0.9102 (m-40) cc_final: 0.8788 (t0) REVERT: O 40 GLN cc_start: 0.7969 (mm110) cc_final: 0.7751 (mm110) REVERT: O 45 PHE cc_start: 0.8543 (t80) cc_final: 0.8334 (t80) REVERT: O 49 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7459 (mm-40) REVERT: O 62 GLN cc_start: 0.9080 (mm110) cc_final: 0.8711 (mm110) REVERT: K 1626 LYS cc_start: 0.7854 (tmtt) cc_final: 0.7329 (tptt) outliers start: 31 outliers final: 19 residues processed: 261 average time/residue: 0.3072 time to fit residues: 111.9166 Evaluate side-chains 255 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 97 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 40 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 117 VAL 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 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 31 GLN Chi-restraints excluded: chain O residue 49 GLN Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14574 Z= 0.243 Angle : 0.591 6.810 20910 Z= 0.342 Chirality : 0.036 0.222 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.657 158.327 4264 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.51 % Allowed : 14.88 % Favored : 80.61 % 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: 0.79 (0.28), residues: 965 helix: 1.64 (0.23), residues: 561 sheet: -0.41 (1.00), residues: 24 loop : -1.14 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.007 0.001 HIS C 31 PHE 0.009 0.001 PHE E 67 TYR 0.042 0.002 TYR B 88 ARG 0.005 0.000 ARG D 79 *********************** 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 281 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 244 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8557 (ttmt) REVERT: A 97 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: A 125 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: A 133 GLU cc_start: 0.8064 (mp0) cc_final: 0.7805 (pm20) REVERT: B 59 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8522 (ttpp) REVERT: B 63 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: B 85 ASP cc_start: 0.8937 (m-30) cc_final: 0.8531 (m-30) REVERT: C 68 ASN cc_start: 0.9111 (m-40) cc_final: 0.8842 (m-40) REVERT: C 84 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: C 104 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8865 (mm-40) REVERT: D 47 GLN cc_start: 0.9370 (mm-40) cc_final: 0.9096 (mm-40) REVERT: E 79 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8369 (ttpp) REVERT: F 52 GLU cc_start: 0.8706 (mp0) cc_final: 0.8430 (mp0) REVERT: F 85 ASP cc_start: 0.9085 (m-30) cc_final: 0.8811 (m-30) REVERT: G 72 ASP cc_start: 0.8883 (m-30) cc_final: 0.8463 (m-30) REVERT: G 73 ASN cc_start: 0.9085 (m-40) cc_final: 0.8807 (t0) REVERT: O 6 LYS cc_start: 0.9353 (mmmt) cc_final: 0.8953 (mmmt) REVERT: O 40 GLN cc_start: 0.8056 (mm110) cc_final: 0.7835 (mm110) REVERT: O 62 GLN cc_start: 0.9052 (mm110) cc_final: 0.8699 (mm110) outliers start: 37 outliers final: 23 residues processed: 257 average time/residue: 0.2712 time to fit residues: 97.4313 Evaluate side-chains 257 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 230 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 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 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 100 LEU 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 H residue 42 TYR 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 31 GLN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 117 optimal weight: 40.0000 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 112 optimal weight: 0.2980 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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** ** 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14574 Z= 0.222 Angle : 0.595 8.832 20910 Z= 0.342 Chirality : 0.036 0.205 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.659 158.661 4264 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.54 % Allowed : 17.44 % Favored : 79.02 % 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: 0.85 (0.28), residues: 965 helix: 1.72 (0.22), residues: 560 sheet: -1.13 (0.81), residues: 34 loop : -1.08 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.005 0.001 HIS G 31 PHE 0.013 0.001 PHE O 45 TYR 0.044 0.002 TYR B 88 ARG 0.005 0.000 ARG D 31 *********************** 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 275 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: A 125 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8653 (pm20) REVERT: A 133 GLU cc_start: 0.8046 (mp0) cc_final: 0.7771 (pm20) REVERT: B 59 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8512 (ttpp) REVERT: B 63 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: B 85 ASP cc_start: 0.8893 (m-30) cc_final: 0.8501 (m-30) REVERT: B 88 TYR cc_start: 0.8933 (m-80) cc_final: 0.8664 (m-80) REVERT: C 84 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8888 (tt0) REVERT: D 34 LYS cc_start: 0.8487 (mmtt) cc_final: 0.7950 (mmtt) REVERT: D 47 GLN cc_start: 0.9369 (mm-40) cc_final: 0.9134 (mm-40) REVERT: F 52 GLU cc_start: 0.8742 (mp0) cc_final: 0.8460 (mp0) REVERT: F 85 ASP cc_start: 0.9076 (m-30) cc_final: 0.8822 (m-30) REVERT: G 51 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9450 (tt) REVERT: G 72 ASP cc_start: 0.8876 (m-30) cc_final: 0.8457 (m-30) REVERT: G 73 ASN cc_start: 0.9068 (m-40) cc_final: 0.8834 (t0) REVERT: H 68 ASP cc_start: 0.9127 (t0) cc_final: 0.8884 (t0) REVERT: O 6 LYS cc_start: 0.9423 (mmmt) cc_final: 0.8998 (mmmt) REVERT: O 40 GLN cc_start: 0.8071 (mm110) cc_final: 0.7860 (mm110) REVERT: O 62 GLN cc_start: 0.9045 (mm110) cc_final: 0.8698 (mm110) outliers start: 29 outliers final: 21 residues processed: 256 average time/residue: 0.2829 time to fit residues: 101.0853 Evaluate side-chains 259 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 233 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 97 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 74 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 117 VAL 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 51 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 TYR 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 31 GLN Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 69 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14574 Z= 0.181 Angle : 0.590 7.521 20910 Z= 0.339 Chirality : 0.036 0.190 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.568 159.596 4264 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.54 % Allowed : 18.41 % Favored : 78.05 % 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: 0.80 (0.28), residues: 965 helix: 1.67 (0.22), residues: 559 sheet: -1.21 (0.77), residues: 34 loop : -1.07 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N1580 HIS 0.005 0.001 HIS G 31 PHE 0.009 0.001 PHE O 45 TYR 0.038 0.001 TYR D 83 ARG 0.004 0.000 ARG K1629 *********************** 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 288 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 259 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8485 (ttmt) cc_final: 0.7985 (ttmt) REVERT: A 125 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: A 133 GLU cc_start: 0.8088 (mp0) cc_final: 0.7782 (pm20) REVERT: B 59 LYS cc_start: 0.9088 (ttmt) cc_final: 0.8618 (ttmm) REVERT: B 63 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: B 85 ASP cc_start: 0.8947 (m-30) cc_final: 0.8577 (m-30) REVERT: C 56 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8265 (mm-30) REVERT: C 84 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.8960 (tt0) REVERT: D 121 TYR cc_start: 0.9365 (t80) cc_final: 0.9145 (t80) REVERT: E 79 LYS cc_start: 0.8819 (ttpp) cc_final: 0.8468 (ptmm) REVERT: E 82 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8166 (mm) REVERT: F 52 GLU cc_start: 0.8730 (mp0) cc_final: 0.8467 (mp0) REVERT: F 85 ASP cc_start: 0.9030 (m-30) cc_final: 0.8807 (m-30) REVERT: G 51 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9457 (tt) REVERT: G 72 ASP cc_start: 0.8895 (m-30) cc_final: 0.8527 (m-30) REVERT: G 75 LYS cc_start: 0.9430 (mmtp) cc_final: 0.8991 (mmmm) REVERT: O 1 MET cc_start: 0.6656 (ttt) cc_final: 0.6081 (mtp) REVERT: O 6 LYS cc_start: 0.9461 (mmmt) cc_final: 0.9246 (mmmm) REVERT: O 62 GLN cc_start: 0.9016 (mm110) cc_final: 0.8559 (mm110) REVERT: K 1626 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7832 (tptt) outliers start: 29 outliers final: 16 residues processed: 272 average time/residue: 0.2839 time to fit residues: 107.8594 Evaluate side-chains 262 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 117 VAL 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 51 LEU Chi-restraints excluded: chain G residue 101 THR 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 31 GLN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain K residue 1622 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 0.0030 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- 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 ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14574 Z= 0.284 Angle : 0.645 9.488 20910 Z= 0.365 Chirality : 0.038 0.225 2371 Planarity : 0.004 0.054 1646 Dihedral : 29.855 158.291 4264 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.66 % Allowed : 19.15 % Favored : 77.20 % 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: 0.80 (0.28), residues: 965 helix: 1.64 (0.22), residues: 560 sheet: -1.23 (0.74), residues: 34 loop : -1.02 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N1580 HIS 0.006 0.001 HIS G 31 PHE 0.010 0.001 PHE E 67 TYR 0.051 0.002 TYR B 88 ARG 0.014 0.000 ARG K1629 *********************** 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 269 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: A 133 GLU cc_start: 0.7902 (mp0) cc_final: 0.7637 (mp0) REVERT: B 59 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8670 (ttpp) REVERT: B 85 ASP cc_start: 0.8849 (m-30) cc_final: 0.8520 (m-30) REVERT: C 84 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8881 (tt0) REVERT: D 121 TYR cc_start: 0.9382 (t80) cc_final: 0.9178 (t80) REVERT: F 85 ASP cc_start: 0.9006 (m-30) cc_final: 0.8769 (m-30) REVERT: G 51 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9468 (tt) REVERT: G 72 ASP cc_start: 0.8754 (m-30) cc_final: 0.8504 (m-30) REVERT: O 6 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9176 (mmmm) REVERT: O 62 GLN cc_start: 0.9082 (mm110) cc_final: 0.8758 (mm110) outliers start: 30 outliers final: 18 residues processed: 255 average time/residue: 0.2797 time to fit residues: 99.8544 Evaluate side-chains 249 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 228 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain E residue 117 VAL 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 51 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR 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 31 GLN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain K residue 1622 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14574 Z= 0.237 Angle : 0.645 10.945 20910 Z= 0.363 Chirality : 0.037 0.233 2371 Planarity : 0.004 0.055 1646 Dihedral : 29.751 158.928 4264 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.05 % Allowed : 20.61 % Favored : 76.34 % 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 (0.28), residues: 965 helix: 1.56 (0.22), residues: 560 sheet: -1.18 (0.76), residues: 34 loop : -1.08 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.050 0.002 TYR B 88 ARG 0.012 0.000 ARG K1629 *********************** REFINEMENT MACRO_CYCLE 9 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 261 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8632 (pm20) REVERT: A 133 GLU cc_start: 0.7987 (mp0) cc_final: 0.7718 (mp0) REVERT: B 59 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8907 (ttpp) REVERT: D 34 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8244 (mmtt) REVERT: D 121 TYR cc_start: 0.9358 (t80) cc_final: 0.9122 (t80) REVERT: F 85 ASP cc_start: 0.9000 (m-30) cc_final: 0.8764 (m-30) REVERT: G 51 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9461 (tt) REVERT: G 72 ASP cc_start: 0.8726 (m-30) cc_final: 0.8516 (m-30) REVERT: O 6 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9146 (mmmm) REVERT: O 62 GLN cc_start: 0.9076 (mm110) cc_final: 0.8747 (mm110) outliers start: 25 outliers final: 18 residues processed: 246 average time/residue: 0.2752 time to fit residues: 95.5408 Evaluate side-chains 248 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 228 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 117 VAL 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 51 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 TYR 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 48 LYS Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain K residue 1622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 120 optimal weight: 40.0000 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- 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** G 89 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14574 Z= 0.214 Angle : 0.650 11.705 20910 Z= 0.363 Chirality : 0.037 0.233 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.684 159.324 4264 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.44 % Allowed : 21.83 % Favored : 75.73 % 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: 0.66 (0.27), residues: 965 helix: 1.51 (0.22), residues: 560 sheet: -1.13 (0.77), residues: 34 loop : -1.08 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.052 0.002 TYR B 88 ARG 0.014 0.000 ARG K1629 ********************** REFINEMENT MACRO_CYCLE 10 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 258 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8638 (ptmm) cc_final: 0.8337 (ptpt) REVERT: A 125 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: A 133 GLU cc_start: 0.8015 (mp0) cc_final: 0.7773 (mp0) REVERT: B 85 ASP cc_start: 0.8905 (m-30) cc_final: 0.8658 (m-30) REVERT: C 89 ASN cc_start: 0.9100 (m-40) cc_final: 0.8683 (m-40) REVERT: D 34 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8296 (mmtt) REVERT: D 83 TYR cc_start: 0.7417 (m-80) cc_final: 0.7201 (t80) REVERT: D 121 TYR cc_start: 0.9340 (t80) cc_final: 0.9120 (t80) REVERT: F 85 ASP cc_start: 0.8950 (m-30) cc_final: 0.8702 (m-30) REVERT: G 51 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9481 (tt) REVERT: G 72 ASP cc_start: 0.8724 (m-30) cc_final: 0.8511 (m-30) REVERT: O 1 MET cc_start: 0.6508 (ttt) cc_final: 0.5946 (mtp) REVERT: O 6 LYS cc_start: 0.9492 (mmmt) cc_final: 0.9134 (mmmm) REVERT: O 62 GLN cc_start: 0.9060 (mm110) cc_final: 0.8629 (mm110) outliers start: 20 outliers final: 16 residues processed: 244 average time/residue: 0.2736 time to fit residues: 94.0293 Evaluate side-chains 250 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 62 ILE Chi-restraints excluded: chain E residue 117 VAL 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 51 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Chi-restraints excluded: chain K residue 1622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 H 84 ASN ** O 41 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 = 0.3334 r_free = 0.3334 target = 0.055342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.037018 restraints weight = 66773.576| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.36 r_work: 0.2528 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14574 Z= 0.219 Angle : 0.650 11.967 20910 Z= 0.363 Chirality : 0.037 0.231 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.690 159.459 4264 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.93 % Allowed : 22.07 % Favored : 75.00 % 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: 1.52 (0.22), residues: 560 sheet: -1.12 (0.77), residues: 34 loop : -1.06 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.028 0.002 TYR B 88 ARG 0.014 0.000 ARG K1629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3060.11 seconds wall clock time: 56 minutes 5.52 seconds (3365.52 seconds total)