Starting phenix.real_space_refine on Tue May 20 13:56:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dz4_27788/05_2025/8dz4_27788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dz4_27788/05_2025/8dz4_27788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dz4_27788/05_2025/8dz4_27788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dz4_27788/05_2025/8dz4_27788.map" model { file = "/net/cci-nas-00/data/ceres_data/8dz4_27788/05_2025/8dz4_27788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dz4_27788/05_2025/8dz4_27788.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.011 sd= 0.156 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 88 5.16 5 C 12766 2.51 5 N 3560 2.21 5 O 3876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20290 Number of models: 1 Model: "" Number of chains: 23 Chain: "I" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 622 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 22, 'TRANS': 65} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "B" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "F" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "O" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "Q" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "T" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "S" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "U" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "X" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "W" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "Z" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "Y" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 986 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Time building chain proxies: 10.93, per 1000 atoms: 0.54 Number of scatterers: 20290 At special positions: 0 Unit cell: (147.2, 113.85, 158.7, 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 88 16.00 O 3876 8.00 N 3560 7.00 C 12766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.02 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 2.4 seconds 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4708 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 66 sheets defined 6.6% alpha, 48.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.817A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.532A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.501A pdb=" N ASN A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.834A pdb=" N THR A 87 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.792A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.909A pdb=" N THR C 87 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.509A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.602A pdb=" N THR O 87 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.518A pdb=" N ASN Q 31 " --> pdb=" O THR Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.753A pdb=" N THR Q 87 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 83 removed outlier: 3.526A pdb=" N ASP T 82 " --> pdb=" O GLN T 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE T 83 " --> pdb=" O SER T 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 79 through 83' Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.554A pdb=" N ASN S 31 " --> pdb=" O THR S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.816A pdb=" N PHE V 83 " --> pdb=" O SER V 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.508A pdb=" N PHE U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 removed outlier: 3.520A pdb=" N THR U 87 " --> pdb=" O VAL U 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 removed outlier: 3.531A pdb=" N PHE W 32 " --> pdb=" O PHE W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 removed outlier: 3.643A pdb=" N THR W 87 " --> pdb=" O VAL W 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 Processing helix chain 'Y' and resid 28 through 32 removed outlier: 3.516A pdb=" N PHE Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.813A pdb=" N THR Y 87 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.575A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.164A pdb=" N VAL L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.164A pdb=" N VAL L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.078A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.011A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.500A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.032A pdb=" N VAL B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.032A pdb=" N VAL B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.585A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.557A pdb=" N VAL A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 88 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 93 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.557A pdb=" N VAL A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 88 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.507A pdb=" N SER D 7 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.187A pdb=" N VAL D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.187A pdb=" N VAL D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.596A pdb=" N MET C 77 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.531A pdb=" N GLY C 10 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.531A pdb=" N GLY C 10 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.533A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.320A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.336A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.336A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.620A pdb=" N SER N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.398A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.521A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.874A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.920A pdb=" N TYR M 102 " --> pdb=" O ARG M 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.613A pdb=" N SER P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER P 67 " --> pdb=" O GLU P 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.692A pdb=" N ILE P 48 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 10 through 12 removed outlier: 3.504A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.622A pdb=" N MET O 77 " --> pdb=" O ASP O 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.926A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.782A pdb=" N TYR O 102 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.613A pdb=" N SER R 22 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.598A pdb=" N VAL R 11 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.598A pdb=" N VAL R 11 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR R 97 " --> pdb=" O GLN R 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 3 through 7 removed outlier: 3.568A pdb=" N MET Q 77 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.407A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET Q 34 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.407A pdb=" N GLY Q 10 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR Q 102 " --> pdb=" O ARG Q 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 4 through 7 removed outlier: 3.541A pdb=" N SER T 22 " --> pdb=" O SER T 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.385A pdb=" N VAL T 11 " --> pdb=" O ASP T 105 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.385A pdb=" N VAL T 11 " --> pdb=" O ASP T 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET S 34 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLY S 10 " --> pdb=" O THR S 110 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR S 102 " --> pdb=" O ARG S 94 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.506A pdb=" N SER V 7 " --> pdb=" O SER V 22 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER V 22 " --> pdb=" O SER V 7 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU V 70 " --> pdb=" O SER V 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 10 through 12 removed outlier: 6.604A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 10 through 12 Processing sheet with id=AF7, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.310A pdb=" N GLY U 10 " --> pdb=" O THR U 110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA U 93 " --> pdb=" O HIS U 35 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N MET U 34 " --> pdb=" O VAL U 50 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.310A pdb=" N GLY U 10 " --> pdb=" O THR U 110 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR U 102 " --> pdb=" O ARG U 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.536A pdb=" N SER X 7 " --> pdb=" O SER X 22 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER X 22 " --> pdb=" O SER X 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU X 70 " --> pdb=" O SER X 67 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'X' and resid 10 through 13 removed outlier: 6.428A pdb=" N LEU X 33 " --> pdb=" O TYR X 49 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR X 49 " --> pdb=" O LEU X 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.548A pdb=" N THR X 97 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'W' and resid 3 through 7 removed outlier: 3.666A pdb=" N MET W 77 " --> pdb=" O ASP W 72 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP W 72 " --> pdb=" O MET W 77 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLY W 10 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N MET W 34 " --> pdb=" O VAL W 50 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLY W 10 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR W 102 " --> pdb=" O ARG W 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 4 through 7 removed outlier: 3.569A pdb=" N SER Z 7 " --> pdb=" O SER Z 22 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER Z 22 " --> pdb=" O SER Z 7 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU Z 70 " --> pdb=" O SER Z 67 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 10 through 13 removed outlier: 6.303A pdb=" N LEU Z 33 " --> pdb=" O TYR Z 49 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR Z 49 " --> pdb=" O LEU Z 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP Z 35 " --> pdb=" O LEU Z 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 10 through 13 removed outlier: 3.566A pdb=" N THR Z 97 " --> pdb=" O GLN Z 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Y' and resid 3 through 7 removed outlier: 3.726A pdb=" N MET Y 77 " --> pdb=" O ASP Y 72 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 10 through 11 removed outlier: 6.273A pdb=" N GLY Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET Y 34 " --> pdb=" O VAL Y 50 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 10 through 11 removed outlier: 6.273A pdb=" N GLY Y 10 " --> pdb=" O THR Y 110 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR Y 102 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 1947 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: 7.74 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6660 1.34 - 1.46: 5226 1.46 - 1.58: 8777 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 20795 Sorted by residual: bond pdb=" CA GLY N 50 " pdb=" C GLY N 50 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.45e+00 bond pdb=" CA GLY N 68 " pdb=" C GLY N 68 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.40e+00 bond pdb=" C VAL Y 12 " pdb=" N GLN Y 13 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.47e-02 4.63e+03 1.97e+00 bond pdb=" N GLY N 68 " pdb=" CA GLY N 68 " ideal model delta sigma weight residual 1.464 1.449 0.016 1.12e-02 7.97e+03 1.96e+00 bond pdb=" N GLY N 50 " pdb=" CA GLY N 50 " ideal model delta sigma weight residual 1.464 1.449 0.016 1.12e-02 7.97e+03 1.93e+00 ... (remaining 20790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 27738 1.73 - 3.46: 415 3.46 - 5.19: 38 5.19 - 6.92: 4 6.92 - 8.65: 4 Bond angle restraints: 28199 Sorted by residual: angle pdb=" C THR T 30 " pdb=" CA THR T 30 " pdb=" CB THR T 30 " ideal model delta sigma weight residual 117.23 110.22 7.01 1.36e+00 5.41e-01 2.66e+01 angle pdb=" C THR R 30 " pdb=" CA THR R 30 " pdb=" CB THR R 30 " ideal model delta sigma weight residual 117.23 110.23 7.00 1.36e+00 5.41e-01 2.65e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" C ALA L 51 " ideal model delta sigma weight residual 114.62 110.41 4.21 1.14e+00 7.69e-01 1.36e+01 angle pdb=" N ALA Z 51 " pdb=" CA ALA Z 51 " pdb=" C ALA Z 51 " ideal model delta sigma weight residual 114.62 110.85 3.77 1.14e+00 7.69e-01 1.10e+01 angle pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " pdb=" CD LYS H 43 " ideal model delta sigma weight residual 111.30 118.70 -7.40 2.30e+00 1.89e-01 1.04e+01 ... (remaining 28194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 10847 17.78 - 35.56: 971 35.56 - 53.34: 249 53.34 - 71.12: 42 71.12 - 88.90: 15 Dihedral angle restraints: 12124 sinusoidal: 4689 harmonic: 7435 Sorted by residual: dihedral pdb=" CA GLY L 50 " pdb=" C GLY L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLY Z 50 " pdb=" C GLY Z 50 " pdb=" N ALA Z 51 " pdb=" CA ALA Z 51 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TYR W 99 " pdb=" C TYR W 99 " pdb=" N ASP W 100 " pdb=" CA ASP W 100 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 12121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1949 0.032 - 0.063: 689 0.063 - 0.095: 189 0.095 - 0.126: 130 0.126 - 0.158: 16 Chirality restraints: 2973 Sorted by residual: chirality pdb=" CA ASP X 82 " pdb=" N ASP X 82 " pdb=" C ASP X 82 " pdb=" CB ASP X 82 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CG LEU X 78 " pdb=" CB LEU X 78 " pdb=" CD1 LEU X 78 " pdb=" CD2 LEU X 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CB THR Y 87 " pdb=" CA THR Y 87 " pdb=" OG1 THR Y 87 " pdb=" CG2 THR Y 87 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 2970 not shown) Planarity restraints: 3684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 58 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO R 59 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 59 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 59 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE V 58 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO V 59 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO V 59 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO V 59 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 72 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" CG ASP C 72 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP C 72 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 72 " 0.010 2.00e-02 2.50e+03 ... (remaining 3681 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1165 2.73 - 3.27: 18567 3.27 - 3.82: 33581 3.82 - 4.36: 41402 4.36 - 4.90: 74129 Nonbonded interactions: 168844 Sorted by model distance: nonbonded pdb=" OG SER X 14 " pdb=" OE2 GLU X 17 " model vdw 2.190 3.040 nonbonded pdb=" O SER R 77 " pdb=" OG SER R 77 " model vdw 2.262 3.040 nonbonded pdb=" OG SER C 7 " pdb=" OG SER C 21 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR X 30 " pdb=" N SER X 31 " model vdw 2.274 3.120 nonbonded pdb=" N GLU E 6 " pdb=" OE1 GLU E 6 " model vdw 2.279 3.120 ... (remaining 168839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.480 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.130 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.002 0.036 20817 Z= 0.121 Angle : 0.550 8.650 28243 Z= 0.318 Chirality : 0.040 0.158 2973 Planarity : 0.004 0.054 3684 Dihedral : 14.794 88.902 7350 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.09 % Allowed : 15.16 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.22 (0.17), residues: 2572 helix: None (None), residues: 0 sheet: 0.23 (0.14), residues: 1210 loop : 0.21 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 103 HIS 0.008 0.001 HIS A 52A PHE 0.012 0.001 PHE O 27 TYR 0.020 0.001 TYR O 102 ARG 0.009 0.001 ARG Z 61 Details of bonding type rmsd hydrogen bonds : bond 0.24622 ( 754) hydrogen bonds : angle 9.26747 ( 1947) SS BOND : bond 0.00239 ( 22) SS BOND : angle 0.61189 ( 44) covalent geometry : bond 0.00228 (20795) covalent geometry : angle 0.55013 (28199) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 353 time to evaluate : 2.076 Fit side-chains REVERT: A 77 MET cc_start: 0.7682 (mtt) cc_final: 0.7040 (mtt) REVERT: C 13 GLN cc_start: 0.8441 (mt0) cc_final: 0.8127 (mt0) REVERT: C 75 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8652 (mtpp) REVERT: F 107 LYS cc_start: 0.7941 (tppt) cc_final: 0.7389 (tppp) REVERT: P 103 LYS cc_start: 0.8477 (tppt) cc_final: 0.8276 (tptt) REVERT: T 79 GLN cc_start: 0.8973 (mp10) cc_final: 0.8742 (mp10) outliers start: 2 outliers final: 2 residues processed: 353 average time/residue: 0.3236 time to fit residues: 172.7983 Evaluate side-chains 326 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain V residue 81 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 101 optimal weight: 0.0770 chunk 195 optimal weight: 0.0570 chunk 75 optimal weight: 0.0000 chunk 119 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.6264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN A 76 ASN M 81 GLN U 3 GLN U 100CASN W 100CASN ** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 56 ASN Y 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096593 restraints weight = 28676.037| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.91 r_work: 0.3029 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20817 Z= 0.140 Angle : 0.537 6.547 28243 Z= 0.291 Chirality : 0.043 0.160 2973 Planarity : 0.004 0.043 3684 Dihedral : 4.080 25.645 2886 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.80 % Allowed : 14.98 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.21 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.34 (0.14), residues: 1210 loop : 0.07 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 103 HIS 0.006 0.001 HIS A 52A PHE 0.011 0.001 PHE M 29 TYR 0.018 0.001 TYR S 90 ARG 0.005 0.000 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 754) hydrogen bonds : angle 5.99646 ( 1947) SS BOND : bond 0.00178 ( 22) SS BOND : angle 0.98091 ( 44) covalent geometry : bond 0.00332 (20795) covalent geometry : angle 0.53648 (28199) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 337 time to evaluate : 2.141 Fit side-chains REVERT: H 99 TYR cc_start: 0.8701 (t80) cc_final: 0.8285 (t80) REVERT: B 91 TYR cc_start: 0.7568 (p90) cc_final: 0.7170 (p90) REVERT: C 91 TYR cc_start: 0.8822 (m-80) cc_final: 0.8576 (m-80) REVERT: M 95 ASP cc_start: 0.8397 (t70) cc_final: 0.8090 (t0) REVERT: P 103 LYS cc_start: 0.8606 (tppt) cc_final: 0.8357 (tptt) REVERT: O 100 ASP cc_start: 0.7558 (m-30) cc_final: 0.7312 (m-30) REVERT: T 81 GLU cc_start: 0.7697 (pm20) cc_final: 0.7459 (pm20) REVERT: S 91 TYR cc_start: 0.9047 (m-80) cc_final: 0.8736 (m-10) REVERT: W 72 ASP cc_start: 0.7697 (p0) cc_final: 0.7327 (t0) outliers start: 39 outliers final: 17 residues processed: 360 average time/residue: 0.3079 time to fit residues: 170.0493 Evaluate side-chains 332 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Y residue 5 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 82 MET Chi-restraints excluded: chain Y residue 100 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 177 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100AHIS O 100AHIS S 100CASN V 1 GLN U 100CASN ** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.091905 restraints weight = 29065.665| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.09 r_work: 0.2940 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 20817 Z= 0.327 Angle : 0.651 8.776 28243 Z= 0.348 Chirality : 0.046 0.156 2973 Planarity : 0.005 0.040 3684 Dihedral : 4.596 27.379 2881 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.86 % Allowed : 15.90 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.20 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.13 (0.14), residues: 1210 loop : -0.27 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 103 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.002 PHE Z 96 TYR 0.027 0.003 TYR L 91 ARG 0.007 0.001 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 754) hydrogen bonds : angle 5.93799 ( 1947) SS BOND : bond 0.00326 ( 22) SS BOND : angle 1.60379 ( 44) covalent geometry : bond 0.00792 (20795) covalent geometry : angle 0.64837 (28199) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 2.127 Fit side-chains REVERT: H 61 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8401 (t70) REVERT: A 100 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.6746 (t0) REVERT: D 104 VAL cc_start: 0.7604 (t) cc_final: 0.7343 (m) REVERT: C 75 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8201 (mtmt) REVERT: N 103 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8073 (tttp) REVERT: V 17 GLU cc_start: 0.7368 (tt0) cc_final: 0.7079 (tt0) REVERT: X 3 VAL cc_start: 0.9174 (t) cc_final: 0.8960 (m) REVERT: X 17 GLU cc_start: 0.7637 (pt0) cc_final: 0.7363 (pm20) REVERT: W 72 ASP cc_start: 0.7698 (p0) cc_final: 0.7389 (t0) REVERT: Y 56 ASN cc_start: 0.8650 (m-40) cc_final: 0.8300 (m-40) outliers start: 62 outliers final: 42 residues processed: 356 average time/residue: 0.3162 time to fit residues: 172.5108 Evaluate side-chains 337 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 293 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 85 GLU Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Z residue 73 LEU Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Y residue 5 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 69 ILE Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 16 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN A 76 ASN D 42 GLN D 92 ASN F 92 ASN Y 76 ASN Y 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.096391 restraints weight = 29073.747| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.90 r_work: 0.3027 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20817 Z= 0.100 Angle : 0.493 7.294 28243 Z= 0.263 Chirality : 0.041 0.147 2973 Planarity : 0.003 0.036 3684 Dihedral : 3.958 24.578 2881 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.71 % Allowed : 17.70 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.04 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.25 (0.14), residues: 1210 loop : -0.19 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.011 0.001 PHE Y 32 TYR 0.012 0.001 TYR C 99 ARG 0.007 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 754) hydrogen bonds : angle 5.17179 ( 1947) SS BOND : bond 0.00294 ( 22) SS BOND : angle 0.83874 ( 44) covalent geometry : bond 0.00236 (20795) covalent geometry : angle 0.49243 (28199) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 357 time to evaluate : 2.104 Fit side-chains REVERT: H 61 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8275 (t70) REVERT: B 92 ASN cc_start: 0.6516 (t0) cc_final: 0.6287 (p0) REVERT: B 96 PHE cc_start: 0.8237 (m-80) cc_final: 0.7955 (m-80) REVERT: C 75 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8235 (mtmt) REVERT: F 54 ARG cc_start: 0.8576 (mtm110) cc_final: 0.8202 (ttm-80) REVERT: O 45 LEU cc_start: 0.8701 (mm) cc_final: 0.8369 (mt) REVERT: O 75 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8504 (mtmt) REVERT: Q 82 MET cc_start: 0.9050 (mtt) cc_final: 0.8644 (mtt) REVERT: T 79 GLN cc_start: 0.8897 (mp10) cc_final: 0.8692 (mp10) REVERT: V 17 GLU cc_start: 0.7316 (tt0) cc_final: 0.7011 (tt0) REVERT: U 100 TYR cc_start: 0.8723 (m-80) cc_final: 0.8510 (m-80) REVERT: X 17 GLU cc_start: 0.7703 (pt0) cc_final: 0.7498 (pm20) REVERT: W 72 ASP cc_start: 0.7695 (p0) cc_final: 0.7335 (t0) outliers start: 37 outliers final: 27 residues processed: 382 average time/residue: 0.3088 time to fit residues: 181.0037 Evaluate side-chains 367 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 339 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 85 GLU Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 81 GLU Chi-restraints excluded: chain Y residue 5 VAL Chi-restraints excluded: chain Y residue 100 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 53 optimal weight: 0.2980 chunk 243 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 239 optimal weight: 6.9990 chunk 85 optimal weight: 0.4980 chunk 201 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN D 42 GLN D 92 ASN Y 76 ASN Y 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095884 restraints weight = 29160.545| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.14 r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20817 Z= 0.140 Angle : 0.514 7.622 28243 Z= 0.272 Chirality : 0.042 0.157 2973 Planarity : 0.004 0.033 3684 Dihedral : 3.966 25.525 2881 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.44 % Allowed : 17.42 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.02 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.27 (0.14), residues: 1210 loop : -0.17 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 103 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE Y 32 TYR 0.019 0.002 TYR H 99 ARG 0.007 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 754) hydrogen bonds : angle 5.08207 ( 1947) SS BOND : bond 0.00114 ( 22) SS BOND : angle 1.01255 ( 44) covalent geometry : bond 0.00338 (20795) covalent geometry : angle 0.51279 (28199) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 2.461 Fit side-chains REVERT: H 61 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8301 (t70) REVERT: H 99 TYR cc_start: 0.8774 (t80) cc_final: 0.8533 (t80) REVERT: B 96 PHE cc_start: 0.8229 (m-80) cc_final: 0.7923 (m-80) REVERT: A 100 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6819 (t0) REVERT: C 75 LYS cc_start: 0.8725 (mtpp) cc_final: 0.8237 (mtmt) REVERT: C 81 GLN cc_start: 0.8371 (tp40) cc_final: 0.7978 (tm-30) REVERT: F 54 ARG cc_start: 0.8626 (mtm110) cc_final: 0.8197 (ttm-80) REVERT: N 1 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: O 45 LEU cc_start: 0.8738 (mm) cc_final: 0.8454 (mt) REVERT: O 75 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8539 (mtmt) REVERT: T 79 GLN cc_start: 0.8875 (mp10) cc_final: 0.8594 (mp10) REVERT: S 91 TYR cc_start: 0.9101 (m-80) cc_final: 0.8621 (m-10) REVERT: V 4 MET cc_start: 0.8572 (mmm) cc_final: 0.8231 (mmm) REVERT: V 17 GLU cc_start: 0.7338 (tt0) cc_final: 0.7045 (tt0) REVERT: U 16 ARG cc_start: 0.8061 (tpp80) cc_final: 0.7812 (mmp80) REVERT: U 100 TYR cc_start: 0.8842 (m-80) cc_final: 0.8632 (m-80) REVERT: X 17 GLU cc_start: 0.7782 (pt0) cc_final: 0.7539 (pm20) REVERT: W 72 ASP cc_start: 0.7695 (p0) cc_final: 0.7335 (t0) REVERT: W 99 TYR cc_start: 0.7914 (t80) cc_final: 0.7540 (t80) outliers start: 53 outliers final: 34 residues processed: 376 average time/residue: 0.3143 time to fit residues: 181.6620 Evaluate side-chains 368 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 331 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 GLN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 85 GLU Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 81 GLU Chi-restraints excluded: chain Y residue 100 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 41 optimal weight: 0.2980 chunk 173 optimal weight: 0.0050 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN A 76 ASN D 42 GLN D 92 ASN X 38 GLN Y 76 ASN Y 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096668 restraints weight = 29027.715| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.09 r_work: 0.3012 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20817 Z= 0.112 Angle : 0.501 8.795 28243 Z= 0.263 Chirality : 0.042 0.166 2973 Planarity : 0.003 0.033 3684 Dihedral : 3.844 24.247 2881 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.44 % Allowed : 17.65 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.04 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.30 (0.14), residues: 1210 loop : -0.13 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 103 HIS 0.005 0.001 HIS E 35 PHE 0.014 0.001 PHE Y 32 TYR 0.016 0.001 TYR H 99 ARG 0.007 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02738 ( 754) hydrogen bonds : angle 4.90821 ( 1947) SS BOND : bond 0.00209 ( 22) SS BOND : angle 0.89996 ( 44) covalent geometry : bond 0.00268 (20795) covalent geometry : angle 0.50054 (28199) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 346 time to evaluate : 2.146 Fit side-chains revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8367 (mp10) cc_final: 0.8018 (mm-40) REVERT: H 61 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8245 (t70) REVERT: H 99 TYR cc_start: 0.8729 (t80) cc_final: 0.8529 (t80) REVERT: B 96 PHE cc_start: 0.8233 (m-80) cc_final: 0.7911 (m-80) REVERT: A 100 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.6849 (t0) REVERT: C 75 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8286 (mtmt) REVERT: F 54 ARG cc_start: 0.8590 (mtm110) cc_final: 0.8193 (ttm-80) REVERT: O 45 LEU cc_start: 0.8698 (mm) cc_final: 0.8372 (mt) REVERT: O 75 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8536 (mtmt) REVERT: T 79 GLN cc_start: 0.8890 (mp10) cc_final: 0.8565 (mp10) REVERT: V 17 GLU cc_start: 0.7449 (tt0) cc_final: 0.7123 (tt0) REVERT: U 16 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7788 (mmp80) REVERT: W 40 THR cc_start: 0.7268 (t) cc_final: 0.6906 (m) REVERT: W 72 ASP cc_start: 0.7717 (p0) cc_final: 0.7376 (t0) outliers start: 53 outliers final: 40 residues processed: 377 average time/residue: 0.3234 time to fit residues: 186.6057 Evaluate side-chains 383 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 GLN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 85 GLU Chi-restraints excluded: chain T residue 3 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 81 GLU Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 69 ILE Chi-restraints excluded: chain Y residue 100 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 62 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 0.0470 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN D 42 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 100AHIS Y 76 ASN Y 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091448 restraints weight = 29443.094| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.12 r_work: 0.2921 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 20817 Z= 0.323 Angle : 0.641 8.434 28243 Z= 0.339 Chirality : 0.046 0.174 2973 Planarity : 0.005 0.040 3684 Dihedral : 4.534 28.742 2881 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.90 % Allowed : 17.83 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.27 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.10 (0.14), residues: 1210 loop : -0.34 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 103 HIS 0.005 0.001 HIS C 35 PHE 0.022 0.002 PHE Z 96 TYR 0.034 0.003 TYR O 102 ARG 0.005 0.001 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 754) hydrogen bonds : angle 5.52395 ( 1947) SS BOND : bond 0.00374 ( 22) SS BOND : angle 1.68692 ( 44) covalent geometry : bond 0.00780 (20795) covalent geometry : angle 0.63849 (28199) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5144 Ramachandran restraints generated. 2572 Oldfield, 0 Emsley, 2572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 329 time to evaluate : 2.121 Fit side-chains REVERT: H 61 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8530 (t70) REVERT: B 96 PHE cc_start: 0.8252 (m-80) cc_final: 0.7991 (m-80) REVERT: A 100 ASN cc_start: 0.7477 (OUTLIER) cc_final: 0.6772 (t0) REVERT: D 49 TYR cc_start: 0.8484 (p90) cc_final: 0.8120 (p90) REVERT: D 70 GLU cc_start: 0.8325 (tp30) cc_final: 0.7996 (tp30) REVERT: D 104 VAL cc_start: 0.7561 (t) cc_final: 0.7312 (m) REVERT: C 75 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8175 (mtmt) REVERT: E 53 ASP cc_start: 0.8992 (p0) cc_final: 0.8645 (p0) REVERT: O 75 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8476 (mtmt) REVERT: T 81 GLU cc_start: 0.8443 (pt0) cc_final: 0.7838 (pm20) REVERT: V 4 MET cc_start: 0.8491 (mmm) cc_final: 0.8232 (mmm) REVERT: V 17 GLU cc_start: 0.7444 (tt0) cc_final: 0.7121 (tt0) REVERT: X 17 GLU cc_start: 0.7936 (pm20) cc_final: 0.7453 (pm20) REVERT: W 72 ASP cc_start: 0.7741 (p0) cc_final: 0.7424 (t0) outliers start: 63 outliers final: 47 residues processed: 372 average time/residue: 0.3191 time to fit residues: 180.1360 Evaluate side-chains 370 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1 GLN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 85 GLU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 81 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 74 THR Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 81 GLU Chi-restraints excluded: chain Y residue 69 ILE Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.735 > 50: distance: 7 - 9: 6.384 distance: 9 - 10: 25.848 distance: 9 - 140: 9.068 distance: 10 - 11: 8.912 distance: 11 - 12: 25.314 distance: 11 - 13: 16.504 distance: 12 - 148: 20.769 distance: 13 - 14: 32.129 distance: 14 - 15: 33.819 distance: 14 - 17: 10.179 distance: 15 - 16: 33.357 distance: 15 - 20: 33.476 distance: 17 - 18: 19.679 distance: 17 - 19: 4.569 distance: 20 - 21: 16.866 distance: 20 - 151: 22.348 distance: 21 - 22: 12.282 distance: 21 - 24: 6.864 distance: 22 - 23: 17.728 distance: 22 - 27: 13.477 distance: 24 - 25: 7.672 distance: 24 - 26: 13.393 distance: 27 - 28: 43.920 distance: 28 - 29: 25.090 distance: 28 - 31: 22.970 distance: 29 - 30: 32.317 distance: 29 - 36: 26.250 distance: 31 - 32: 7.656 distance: 32 - 33: 13.310 distance: 33 - 35: 3.986 distance: 36 - 37: 39.522 distance: 36 - 42: 24.815 distance: 37 - 38: 6.578 distance: 37 - 40: 17.623 distance: 38 - 39: 7.736 distance: 38 - 43: 11.728 distance: 40 - 41: 34.708 distance: 41 - 42: 20.299 distance: 43 - 44: 12.184 distance: 44 - 45: 16.848 distance: 45 - 46: 3.185 distance: 45 - 47: 5.132 distance: 47 - 48: 4.107 distance: 48 - 49: 6.663 distance: 48 - 51: 19.841 distance: 49 - 50: 25.293 distance: 49 - 58: 20.154 distance: 51 - 52: 33.259 distance: 52 - 53: 18.145 distance: 53 - 54: 8.412 distance: 54 - 55: 18.529 distance: 55 - 56: 13.077 distance: 55 - 57: 27.543 distance: 58 - 59: 20.412 distance: 59 - 60: 16.651 distance: 59 - 62: 18.716 distance: 60 - 61: 12.121 distance: 60 - 64: 25.007 distance: 62 - 63: 23.734 distance: 64 - 65: 16.834 distance: 64 - 113: 28.765 distance: 65 - 66: 19.201 distance: 65 - 68: 12.623 distance: 66 - 67: 10.626 distance: 66 - 72: 15.845 distance: 67 - 110: 16.016 distance: 68 - 69: 12.449 distance: 69 - 70: 24.403 distance: 69 - 71: 14.449 distance: 72 - 73: 6.108 distance: 73 - 74: 7.854 distance: 73 - 76: 4.498 distance: 74 - 75: 11.250 distance: 74 - 83: 27.875 distance: 76 - 77: 7.267 distance: 77 - 78: 8.874 distance: 78 - 79: 8.389 distance: 79 - 80: 10.109 distance: 80 - 81: 12.818 distance: 80 - 82: 8.915