Starting phenix.real_space_refine on Sat Dec 9 07:36:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nca_12264/12_2023/7nca_12264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nca_12264/12_2023/7nca_12264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nca_12264/12_2023/7nca_12264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nca_12264/12_2023/7nca_12264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nca_12264/12_2023/7nca_12264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nca_12264/12_2023/7nca_12264.pdb" } resolution = 3.47 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: 4 Type Number sf(0) Gaussians C 3180 2.51 5 N 876 2.21 5 O 996 1.98 5 H 5376 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 46": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" 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: 10428 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "G" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "L" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 869 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 4.70, per 1000 atoms: 0.45 Number of scatterers: 10428 At special positions: 0 Unit cell: (80.94, 112.86, 52.44, 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) O 996 8.00 N 876 7.00 C 3180 6.00 H 5376 1.00 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: 7.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 47.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 44 removed outlier: 6.651A pdb=" N LEU A 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY E 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS E 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER A 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 39 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 40 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 41 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER F 42 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 43 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR F 44 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR F 39 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL K 40 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER K 42 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS F 43 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR K 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU J 38 " --> pdb=" O TYR K 39 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLY K 41 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL J 40 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS K 43 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER J 42 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR J 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N SER L 42 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY J 41 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N THR L 44 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LYS J 43 " --> pdb=" O THR L 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.046A pdb=" N VAL A 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY F 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N HIS A 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA F 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 48 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N GLY K 51 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N HIS F 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL J 49 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL K 52 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY J 51 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL J 48 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N GLY L 51 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N HIS J 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.624A pdb=" N THR A 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR F 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA K 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL F 55 " --> pdb=" O ALA K 56 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL J 55 " --> pdb=" O ALA L 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 61 through 66 removed outlier: 7.126A pdb=" N GLU A 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N THR F 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL A 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL F 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN A 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU F 61 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N THR K 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL F 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N VAL K 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN F 65 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN J 62 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL K 63 " --> pdb=" O GLN J 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR J 64 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN K 65 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL J 66 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU J 61 " --> pdb=" O GLN L 62 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR L 64 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL J 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL L 66 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN J 65 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.692A pdb=" N VAL A 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL F 71 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR K 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL J 70 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.764A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 76 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN F 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA F 78 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN K 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR J 75 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ALA K 78 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL J 77 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN L 79 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 82 through 83 removed outlier: 7.168A pdb=" N VAL A 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL F 82 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL J 82 " --> pdb=" O GLU L 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.933A pdb=" N ILE A 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 89 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA F 89 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE J 88 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA J 89 " --> pdb=" O ILE L 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.973A pdb=" N GLY A 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N LYS E 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY F 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL F 95 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 96 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY K 93 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE F 94 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL K 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N THR J 92 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL K 95 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N PHE J 94 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR J 92 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL L 95 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE J 94 " --> pdb=" O VAL L 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 38 through 44 removed outlier: 3.588A pdb=" N SER B 42 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N SER D 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR D 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS B 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR D 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU G 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.957A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LYS G 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY G 47 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL H 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 49 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS H 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL H 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR G 44 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N GLY I 47 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU G 46 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N VAL I 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL G 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY I 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N HIS G 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.468A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA G 56 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.731A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLU B 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR D 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL D 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU D 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR H 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL H 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN D 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN G 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN H 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR G 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU G 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR I 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL I 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.638A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR H 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.708A pdb=" N THR B 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ALA C 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL D 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 76 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL H 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN H 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR G 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ALA H 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL G 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 82 through 83 removed outlier: 7.503A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU G 83 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL G 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 88 through 89 removed outlier: 3.793A pdb=" N ALA B 89 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 89 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 89 " --> pdb=" O ILE I 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 92 through 96 removed outlier: 7.057A pdb=" N GLY B 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N LYS C 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY D 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 95 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 96 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 93 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE H 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL D 95 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LYS H 96 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLY G 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N LYS H 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL G 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY I 93 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE G 94 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL I 95 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 96 " --> pdb=" O VAL I 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 36 hydrogen bonds defined for protein. 108 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: 3.17 Time building geometry restraints manager: 7.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.04: 1200 1.04 - 1.16: 4176 1.16 - 1.29: 866 1.29 - 1.42: 1090 1.42 - 1.55: 3120 Bond restraints: 10452 Sorted by residual: bond pdb=" N THR F 72 " pdb=" H THR F 72 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N THR K 75 " pdb=" H THR K 75 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLY F 41 " pdb=" H GLY F 41 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 TYR J 39 " pdb=" HE1 TYR J 39 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLY L 67 " pdb=" H GLY L 67 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 10447 not shown) Histogram of bond angle deviations from ideal: 103.72 - 108.61: 4639 108.61 - 113.51: 8774 113.51 - 118.40: 2062 118.40 - 123.30: 2839 123.30 - 128.19: 718 Bond angle restraints: 19032 Sorted by residual: angle pdb=" N ALA C 90 " pdb=" CA ALA C 90 " pdb=" C ALA C 90 " ideal model delta sigma weight residual 110.06 116.62 -6.56 1.43e+00 4.89e-01 2.10e+01 angle pdb=" CB HIS G 50 " pdb=" CG HIS G 50 " pdb=" CD2 HIS G 50 " ideal model delta sigma weight residual 131.20 125.30 5.90 1.30e+00 5.92e-01 2.06e+01 angle pdb=" OE1 GLN A 79 " pdb=" CD GLN A 79 " pdb=" NE2 GLN A 79 " ideal model delta sigma weight residual 122.60 118.08 4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" OE1 GLN D 62 " pdb=" CD GLN D 62 " pdb=" NE2 GLN D 62 " ideal model delta sigma weight residual 122.60 118.19 4.41 1.00e+00 1.00e+00 1.95e+01 angle pdb=" CB HIS C 50 " pdb=" CG HIS C 50 " pdb=" CD2 HIS C 50 " ideal model delta sigma weight residual 131.20 125.52 5.68 1.30e+00 5.92e-01 1.91e+01 ... (remaining 19027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 4106 16.11 - 32.23: 108 32.23 - 48.34: 66 48.34 - 64.46: 210 64.46 - 80.57: 34 Dihedral angle restraints: 4524 sinusoidal: 2400 harmonic: 2124 Sorted by residual: dihedral pdb=" CA ALA F 89 " pdb=" C ALA F 89 " pdb=" N ALA F 90 " pdb=" CA ALA F 90 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ALA C 89 " pdb=" C ALA C 89 " pdb=" N ALA C 90 " pdb=" CA ALA C 90 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ALA A 89 " pdb=" C ALA A 89 " pdb=" N ALA A 90 " pdb=" CA ALA A 90 " ideal model delta harmonic sigma weight residual -180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 4521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 354 0.045 - 0.089: 294 0.089 - 0.134: 179 0.134 - 0.179: 74 0.179 - 0.223: 11 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA VAL B 82 " pdb=" N VAL B 82 " pdb=" C VAL B 82 " pdb=" CB VAL B 82 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA GLU G 57 " pdb=" N GLU G 57 " pdb=" C GLU G 57 " pdb=" CB GLU G 57 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA GLU F 57 " pdb=" N GLU F 57 " pdb=" C GLU F 57 " pdb=" CB GLU F 57 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.82e-01 ... (remaining 909 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 39 " -0.081 2.00e-02 2.50e+03 3.56e-02 3.81e+01 pdb=" CG TYR E 39 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR E 39 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR E 39 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR E 39 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR E 39 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR E 39 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 39 " -0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR E 39 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 TYR E 39 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR E 39 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR E 39 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 89 " -0.031 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" N ALA G 90 " 0.100 2.00e-02 2.50e+03 pdb=" CA ALA G 90 " -0.028 2.00e-02 2.50e+03 pdb=" H ALA G 90 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 89 " 0.031 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" N ALA A 90 " -0.098 2.00e-02 2.50e+03 pdb=" CA ALA A 90 " 0.028 2.00e-02 2.50e+03 pdb=" H ALA A 90 " 0.039 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.34: 1284 2.34 - 2.88: 20496 2.88 - 3.42: 21178 3.42 - 3.96: 25276 3.96 - 4.50: 38471 Nonbonded interactions: 106705 Sorted by model distance: nonbonded pdb=" O LYS H 43 " pdb=" HG1 THR H 44 " model vdw 1.803 1.850 nonbonded pdb=" O ALA K 53 " pdb=" HG1 THR K 54 " model vdw 1.811 1.850 nonbonded pdb=" O LYS G 43 " pdb=" HG1 THR G 44 " model vdw 1.819 1.850 nonbonded pdb=" O ALA J 53 " pdb=" HG1 THR J 54 " model vdw 1.822 1.850 nonbonded pdb=" OE2 GLU A 57 " pdb=" HZ2 LYS A 58 " model vdw 1.826 1.850 ... (remaining 106700 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' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.180 Extract box with map and model: 3.960 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 33.340 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.012 0.037 5076 Z= 0.803 Angle : 2.035 7.221 6864 Z= 1.305 Chirality : 0.080 0.223 912 Planarity : 0.007 0.040 840 Dihedral : 10.639 80.570 1716 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.19 % Allowed : 0.97 % Favored : 98.84 % 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: -2.04 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.035 0.008 PHE E 94 TYR 0.069 0.018 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.5450 time to fit residues: 81.2442 Evaluate side-chains 90 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1641 time to fit residues: 1.2462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5076 Z= 0.228 Angle : 0.572 3.794 6864 Z= 0.330 Chirality : 0.053 0.141 912 Planarity : 0.002 0.007 840 Dihedral : 5.261 18.772 732 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.58 % Allowed : 9.11 % Favored : 90.31 % 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: -2.73 (0.20), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.15), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 50 PHE 0.014 0.003 PHE L 94 TYR 0.008 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.855 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 0.4281 time to fit residues: 52.1263 Evaluate side-chains 84 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1065 time to fit residues: 1.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5076 Z= 0.171 Angle : 0.482 3.980 6864 Z= 0.274 Chirality : 0.053 0.144 912 Planarity : 0.001 0.006 840 Dihedral : 4.663 17.547 732 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.97 % Allowed : 9.30 % Favored : 89.73 % 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: -3.05 (0.19), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.14), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.009 0.002 PHE I 94 TYR 0.004 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.835 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.4169 time to fit residues: 48.4195 Evaluate side-chains 86 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4428 time to fit residues: 2.5568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5076 Z= 0.188 Angle : 0.480 3.676 6864 Z= 0.272 Chirality : 0.053 0.146 912 Planarity : 0.001 0.006 840 Dihedral : 4.542 17.076 732 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.36 % Allowed : 8.91 % Favored : 89.73 % 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: -3.13 (0.20), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.15), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 50 PHE 0.013 0.003 PHE K 94 TYR 0.006 0.001 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.849 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.3781 time to fit residues: 42.2344 Evaluate side-chains 86 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1296 time to fit residues: 2.0980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5076 Z= 0.116 Angle : 0.419 4.406 6864 Z= 0.231 Chirality : 0.053 0.141 912 Planarity : 0.001 0.003 840 Dihedral : 4.200 15.090 732 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.39 % Allowed : 9.69 % Favored : 89.92 % 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: -3.03 (0.20), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.16), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.006 0.001 PHE F 94 TYR 0.005 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.736 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 81 average time/residue: 0.3548 time to fit residues: 37.1283 Evaluate side-chains 79 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1080 time to fit residues: 1.3606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5076 Z= 0.211 Angle : 0.481 4.070 6864 Z= 0.274 Chirality : 0.053 0.149 912 Planarity : 0.001 0.006 840 Dihedral : 4.416 17.162 732 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.58 % Allowed : 10.08 % Favored : 89.34 % 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: -3.13 (0.21), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.16), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.010 0.003 PHE L 94 TYR 0.005 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.830 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 77 average time/residue: 0.3668 time to fit residues: 36.3451 Evaluate side-chains 79 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1226 time to fit residues: 1.5881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5076 Z= 0.129 Angle : 0.424 3.935 6864 Z= 0.237 Chirality : 0.053 0.142 912 Planarity : 0.001 0.003 840 Dihedral : 4.219 16.188 732 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.39 % Allowed : 10.47 % Favored : 89.15 % 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: -3.07 (0.21), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.16), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.007 0.002 PHE J 94 TYR 0.005 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.891 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.3919 time to fit residues: 37.9771 Evaluate side-chains 75 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1094 time to fit residues: 1.1561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5076 Z= 0.171 Angle : 0.447 3.960 6864 Z= 0.252 Chirality : 0.053 0.146 912 Planarity : 0.001 0.004 840 Dihedral : 4.273 16.700 732 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.58 % Allowed : 10.66 % Favored : 88.76 % 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: -3.09 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.010 0.002 PHE C 94 TYR 0.004 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.847 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.4002 time to fit residues: 38.7688 Evaluate side-chains 75 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1217 time to fit residues: 1.5431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5076 Z= 0.151 Angle : 0.435 3.878 6864 Z= 0.244 Chirality : 0.053 0.146 912 Planarity : 0.001 0.004 840 Dihedral : 4.234 16.487 732 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % 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: -3.07 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.004 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.779 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3568 time to fit residues: 34.3796 Evaluate side-chains 73 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5076 Z= 0.193 Angle : 0.460 3.887 6864 Z= 0.261 Chirality : 0.053 0.147 912 Planarity : 0.001 0.004 840 Dihedral : 4.335 17.106 732 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.39 % Allowed : 11.05 % Favored : 88.57 % 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: -3.16 (0.22), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.010 0.003 PHE I 94 TYR 0.005 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.742 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 76 average time/residue: 0.3907 time to fit residues: 37.9018 Evaluate side-chains 76 residues out of total 516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1087 time to fit residues: 1.3813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.5980 chunk 8 optimal weight: 0.0020 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 0.0770 chunk 41 optimal weight: 2.9990 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.117520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096474 restraints weight = 23012.767| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.32 r_work: 0.3496 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5076 Z= 0.118 Angle : 0.414 3.891 6864 Z= 0.229 Chirality : 0.053 0.140 912 Planarity : 0.001 0.003 840 Dihedral : 4.096 15.504 732 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % 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: -3.03 (0.23), residues: 708 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.17), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.006 0.001 PHE F 94 TYR 0.003 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2911.60 seconds wall clock time: 52 minutes 1.88 seconds (3121.88 seconds total)