Starting phenix.real_space_refine on Sat Dec 9 19:21:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/12_2023/6c53_7342.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/12_2023/6c53_7342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/12_2023/6c53_7342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/12_2023/6c53_7342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/12_2023/6c53_7342.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c53_7342/12_2023/6c53_7342.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.010 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 7359 2.51 5 N 2112 2.21 5 O 2530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12023 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "C" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "D" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "E" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "F" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "G" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "H" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "I" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "J" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "K" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1093 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Time building chain proxies: 8.90, per 1000 atoms: 0.74 Number of scatterers: 12023 At special positions: 0 Unit cell: (82.95, 82.95, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 2530 8.00 N 2112 7.00 C 7359 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 61 " distance=2.03 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 61 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 3.8 seconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 43 sheets defined 3.8% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL B 28 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL H 28 " --> pdb=" O ASP H 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL I 28 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 29 removed outlier: 3.628A pdb=" N VAL J 28 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 removed outlier: 3.627A pdb=" N VAL K 28 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN A 6 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL B 156 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 74 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL B 37 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU A 15 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 23 removed outlier: 3.603A pdb=" N ALA A 22 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN A 59 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN A 129 " --> pdb=" O ASN A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 122 through 123 removed outlier: 3.577A pdb=" N LEU A 74 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL A 156 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN C 6 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN B 6 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL D 156 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 74 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 37 removed outlier: 8.330A pdb=" N VAL D 37 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 15 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA B 22 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN B 59 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 129 " --> pdb=" O ASN B 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA C 22 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN C 59 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN C 129 " --> pdb=" O ASN C 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB4, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU C 74 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL C 156 " --> pdb=" O ASN E 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN E 6 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN D 6 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL F 156 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU F 74 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 36 through 37 removed outlier: 8.332A pdb=" N VAL F 37 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 15 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA D 22 " --> pdb=" O ASN D 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN D 59 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN D 129 " --> pdb=" O ASN D 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA E 22 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASN E 59 " --> pdb=" O ASN E 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN E 129 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 36 through 37 Processing sheet with id=AC3, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 123 removed outlier: 3.575A pdb=" N LEU E 74 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL E 156 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN G 6 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN F 6 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL H 156 " --> pdb=" O ASN F 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 74 " --> pdb=" O THR H 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL H 37 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU F 15 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA F 22 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN F 59 " --> pdb=" O ASN F 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN F 129 " --> pdb=" O ASN F 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AC9, first strand: chain 'G' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA G 22 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN G 59 " --> pdb=" O ASN G 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN G 129 " --> pdb=" O ASN G 59 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 36 through 37 Processing sheet with id=AD2, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AD3, first strand: chain 'G' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU G 74 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL G 156 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASN I 6 " --> pdb=" O VAL G 156 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 10 removed outlier: 5.328A pdb=" N ASN H 6 " --> pdb=" O VAL J 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL J 156 " --> pdb=" O ASN H 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 74 " --> pdb=" O THR J 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 36 through 37 removed outlier: 8.331A pdb=" N VAL J 37 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU H 15 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA H 22 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN H 59 " --> pdb=" O ASN H 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN H 129 " --> pdb=" O ASN H 59 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 52 through 54 Processing sheet with id=AD8, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.602A pdb=" N ALA I 22 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN I 59 " --> pdb=" O ASN I 129 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN I 129 " --> pdb=" O ASN I 59 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 36 through 37 Processing sheet with id=AE1, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AE2, first strand: chain 'I' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU I 74 " --> pdb=" O THR I 153 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL I 156 " --> pdb=" O ASN K 6 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN K 6 " --> pdb=" O VAL I 156 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA J 22 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN J 59 " --> pdb=" O ASN J 129 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN J 129 " --> pdb=" O ASN J 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 52 through 54 Processing sheet with id=AE5, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.603A pdb=" N ALA K 22 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ASN K 59 " --> pdb=" O ASN K 129 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN K 129 " --> pdb=" O ASN K 59 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AE7, first strand: chain 'K' and resid 122 through 123 removed outlier: 3.576A pdb=" N LEU K 74 " --> pdb=" O THR K 153 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4246 1.34 - 1.46: 2492 1.46 - 1.57: 5395 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 12155 Sorted by residual: bond pdb=" N THR E 3 " pdb=" CA THR E 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 bond pdb=" N THR I 3 " pdb=" CA THR I 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" N THR J 3 " pdb=" CA THR J 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.46e+00 bond pdb=" N THR G 3 " pdb=" CA THR G 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.46e+00 bond pdb=" N THR B 3 " pdb=" CA THR B 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.44e+00 ... (remaining 12150 not shown) Histogram of bond angle deviations from ideal: 102.78 - 108.47: 608 108.47 - 114.17: 6729 114.17 - 119.86: 3125 119.86 - 125.55: 6082 125.55 - 131.24: 66 Bond angle restraints: 16610 Sorted by residual: angle pdb=" CA GLY J 75 " pdb=" C GLY J 75 " pdb=" N THR J 76 " ideal model delta sigma weight residual 115.34 117.69 -2.35 8.40e-01 1.42e+00 7.84e+00 angle pdb=" CA GLY A 75 " pdb=" C GLY A 75 " pdb=" N THR A 76 " ideal model delta sigma weight residual 115.34 117.66 -2.32 8.40e-01 1.42e+00 7.64e+00 angle pdb=" CA GLY E 75 " pdb=" C GLY E 75 " pdb=" N THR E 76 " ideal model delta sigma weight residual 115.34 117.66 -2.32 8.40e-01 1.42e+00 7.63e+00 angle pdb=" CA GLY B 75 " pdb=" C GLY B 75 " pdb=" N THR B 76 " ideal model delta sigma weight residual 115.34 117.65 -2.31 8.40e-01 1.42e+00 7.59e+00 angle pdb=" CA GLY C 75 " pdb=" C GLY C 75 " pdb=" N THR C 76 " ideal model delta sigma weight residual 115.34 117.65 -2.31 8.40e-01 1.42e+00 7.54e+00 ... (remaining 16605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 6721 14.78 - 29.55: 319 29.55 - 44.33: 22 44.33 - 59.10: 11 59.10 - 73.88: 11 Dihedral angle restraints: 7084 sinusoidal: 2277 harmonic: 4807 Sorted by residual: dihedral pdb=" CA SER H 50 " pdb=" C SER H 50 " pdb=" N ALA H 51 " pdb=" CA ALA H 51 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta harmonic sigma weight residual 180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA SER I 50 " pdb=" C SER I 50 " pdb=" N ALA I 51 " pdb=" CA ALA I 51 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1291 0.038 - 0.075: 553 0.075 - 0.113: 140 0.113 - 0.151: 84 0.151 - 0.189: 11 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CA ILE E 56 " pdb=" N ILE E 56 " pdb=" C ILE E 56 " pdb=" CB ILE E 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA ILE K 56 " pdb=" N ILE K 56 " pdb=" C ILE K 56 " pdb=" CB ILE K 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA ILE B 56 " pdb=" N ILE B 56 " pdb=" C ILE B 56 " pdb=" CB ILE B 56 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 2076 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 144 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO K 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO K 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 145 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 144 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO I 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO I 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 145 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 144 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO C 145 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 145 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 145 " 0.029 5.00e-02 4.00e+02 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 806 2.70 - 3.25: 13039 3.25 - 3.80: 19384 3.80 - 4.35: 27058 4.35 - 4.90: 42511 Nonbonded interactions: 102798 Sorted by model distance: nonbonded pdb=" O VAL I 156 " pdb=" OG1 THR K 4 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR H 4 " pdb=" O VAL J 156 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR B 4 " pdb=" O VAL D 156 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR A 4 " pdb=" O VAL B 156 " model vdw 2.150 2.440 nonbonded pdb=" O VAL E 156 " pdb=" OG1 THR G 4 " model vdw 2.150 2.440 ... (remaining 102793 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 41.770 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12155 Z= 0.400 Angle : 0.923 6.365 16610 Z= 0.554 Chirality : 0.050 0.189 2079 Planarity : 0.004 0.051 2222 Dihedral : 9.181 73.877 3971 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.15), residues: 1694 helix: None (None), residues: 0 sheet: -2.78 (0.18), residues: 473 loop : -3.27 (0.14), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 11 PHE 0.008 0.002 PHE E 73 TYR 0.005 0.002 TYR H 137 ARG 0.002 0.001 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2484 time to fit residues: 123.1674 Evaluate side-chains 163 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 50.0000 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 50.0000 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 overall best weight: 12.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN E 36 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12155 Z= 0.285 Angle : 0.625 5.745 16610 Z= 0.349 Chirality : 0.043 0.139 2079 Planarity : 0.004 0.039 2222 Dihedral : 6.033 21.317 1760 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.08 % Allowed : 1.64 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.18), residues: 1694 helix: -3.25 (0.46), residues: 66 sheet: -1.69 (0.21), residues: 473 loop : -2.43 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 11 PHE 0.016 0.002 PHE B 118 TYR 0.015 0.003 TYR E 137 ARG 0.008 0.002 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 256 average time/residue: 0.2098 time to fit residues: 80.9426 Evaluate side-chains 147 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 50.0000 chunk 46 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 41 optimal weight: 50.0000 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 50.0000 chunk 133 optimal weight: 30.0000 chunk 148 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 overall best weight: 16.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 12155 Z= 0.328 Angle : 0.623 5.865 16610 Z= 0.344 Chirality : 0.042 0.136 2079 Planarity : 0.004 0.039 2222 Dihedral : 5.774 21.076 1760 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.18), residues: 1694 helix: -3.05 (0.50), residues: 66 sheet: -1.22 (0.21), residues: 473 loop : -2.15 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 11 PHE 0.017 0.002 PHE H 118 TYR 0.014 0.003 TYR I 137 ARG 0.005 0.001 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2339 time to fit residues: 73.4990 Evaluate side-chains 125 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.372 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 40.0000 chunk 112 optimal weight: 50.0000 chunk 77 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 71 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 150 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 40.0000 chunk 42 optimal weight: 30.0000 overall best weight: 24.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 12155 Z= 0.467 Angle : 0.731 8.136 16610 Z= 0.404 Chirality : 0.043 0.202 2079 Planarity : 0.005 0.037 2222 Dihedral : 6.531 25.447 1760 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.08 % Allowed : 2.87 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1694 helix: -3.16 (0.48), residues: 66 sheet: -1.07 (0.22), residues: 451 loop : -2.20 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 11 PHE 0.018 0.003 PHE K 133 TYR 0.014 0.003 TYR E 137 ARG 0.008 0.002 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2114 time to fit residues: 54.6826 Evaluate side-chains 119 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 136 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 143 optimal weight: 40.0000 chunk 40 optimal weight: 50.0000 overall best weight: 9.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN I 30 GLN I 57 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12155 Z= 0.226 Angle : 0.562 6.431 16610 Z= 0.305 Chirality : 0.041 0.129 2079 Planarity : 0.003 0.038 2222 Dihedral : 5.303 19.130 1760 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.18), residues: 1694 helix: -2.83 (0.54), residues: 66 sheet: -0.76 (0.23), residues: 451 loop : -1.96 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 11 PHE 0.021 0.002 PHE A 154 TYR 0.010 0.002 TYR E 137 ARG 0.004 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2241 time to fit residues: 67.7342 Evaluate side-chains 126 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 20.0000 chunk 143 optimal weight: 50.0000 chunk 31 optimal weight: 40.0000 chunk 93 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 chunk 159 optimal weight: 50.0000 chunk 132 optimal weight: 50.0000 chunk 73 optimal weight: 30.0000 chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 40.0000 chunk 83 optimal weight: 50.0000 overall best weight: 27.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN K 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 12155 Z= 0.504 Angle : 0.755 9.049 16610 Z= 0.416 Chirality : 0.043 0.144 2079 Planarity : 0.004 0.035 2222 Dihedral : 6.567 28.356 1760 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 32.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.18), residues: 1694 helix: -2.99 (0.50), residues: 66 sheet: -1.06 (0.22), residues: 473 loop : -2.26 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS F 82 PHE 0.023 0.003 PHE A 54 TYR 0.016 0.002 TYR E 137 ARG 0.008 0.002 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2109 time to fit residues: 49.5560 Evaluate side-chains 116 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 134 optimal weight: 40.0000 chunk 89 optimal weight: 30.0000 chunk 159 optimal weight: 40.0000 chunk 99 optimal weight: 50.0000 chunk 96 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** J 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12155 Z= 0.207 Angle : 0.583 7.109 16610 Z= 0.314 Chirality : 0.041 0.133 2079 Planarity : 0.003 0.037 2222 Dihedral : 5.437 20.136 1760 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.18), residues: 1694 helix: -2.73 (0.55), residues: 66 sheet: -0.84 (0.23), residues: 451 loop : -1.95 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 82 PHE 0.024 0.002 PHE G 154 TYR 0.014 0.002 TYR F 158 ARG 0.002 0.001 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2224 time to fit residues: 57.5737 Evaluate side-chains 136 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 30.0000 chunk 94 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 108 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 144 optimal weight: 40.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 GLN ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12155 Z= 0.217 Angle : 0.573 6.155 16610 Z= 0.305 Chirality : 0.041 0.128 2079 Planarity : 0.003 0.033 2222 Dihedral : 5.273 20.599 1760 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1694 helix: -2.55 (0.58), residues: 66 sheet: -0.70 (0.23), residues: 451 loop : -1.81 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 11 PHE 0.026 0.002 PHE H 54 TYR 0.012 0.002 TYR E 137 ARG 0.003 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2235 time to fit residues: 56.1632 Evaluate side-chains 132 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 50.0000 chunk 139 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 89 optimal weight: 50.0000 chunk 64 optimal weight: 10.0000 chunk 116 optimal weight: 30.0000 chunk 45 optimal weight: 50.0000 chunk 133 optimal weight: 30.0000 chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 50.0000 chunk 97 optimal weight: 50.0000 overall best weight: 16.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 HIS ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12155 Z= 0.326 Angle : 0.646 8.035 16610 Z= 0.347 Chirality : 0.041 0.136 2079 Planarity : 0.003 0.033 2222 Dihedral : 5.734 22.619 1760 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.19), residues: 1694 helix: -2.42 (0.60), residues: 66 sheet: -0.88 (0.22), residues: 473 loop : -1.93 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 11 PHE 0.015 0.002 PHE C 133 TYR 0.018 0.002 TYR A 137 ARG 0.006 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2186 time to fit residues: 51.0175 Evaluate side-chains 121 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 74 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 164 optimal weight: 40.0000 chunk 151 optimal weight: 20.0000 chunk 130 optimal weight: 50.0000 chunk 13 optimal weight: 8.9990 chunk 101 optimal weight: 50.0000 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12155 Z= 0.183 Angle : 0.578 8.574 16610 Z= 0.303 Chirality : 0.041 0.145 2079 Planarity : 0.003 0.034 2222 Dihedral : 5.044 21.971 1760 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.19), residues: 1694 helix: -2.18 (0.61), residues: 66 sheet: -0.65 (0.22), residues: 473 loop : -1.76 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 11 PHE 0.015 0.002 PHE D 118 TYR 0.015 0.002 TYR A 137 ARG 0.002 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2084 time to fit residues: 54.6471 Evaluate side-chains 131 residues out of total 1221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 30.0000 chunk 40 optimal weight: 40.0000 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 54 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 24 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 overall best weight: 14.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.064961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058721 restraints weight = 61502.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.060368 restraints weight = 36578.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061484 restraints weight = 23760.738| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12155 Z= 0.303 Angle : 0.632 9.064 16610 Z= 0.340 Chirality : 0.041 0.150 2079 Planarity : 0.003 0.037 2222 Dihedral : 5.566 22.411 1760 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 26.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.19), residues: 1694 helix: -2.20 (0.63), residues: 66 sheet: -0.73 (0.22), residues: 473 loop : -1.81 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 11 PHE 0.015 0.002 PHE D 118 TYR 0.010 0.002 TYR A 137 ARG 0.008 0.001 ARG G 136 =============================================================================== Job complete usr+sys time: 2046.66 seconds wall clock time: 39 minutes 4.81 seconds (2344.81 seconds total)