Starting phenix.real_space_refine on Tue Jun 17 14:26:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dz4_27788/06_2025/8dz4_27788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dz4_27788/06_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_27788/06_2025/8dz4_27788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dz4_27788/06_2025/8dz4_27788.map" model { file = "/net/cci-nas-00/data/ceres_data/8dz4_27788/06_2025/8dz4_27788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dz4_27788/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.68, per 1000 atoms: 0.58 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: 4.54 Conformation dependent library (CDL) restraints added in 2.6 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: 4.25 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: 7.65 Time building geometry restraints manager: 5.64 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: 0.790 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: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.350 Find NCS groups from input model: 0.760 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.960 ------------------------------------------------------------------------------- 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 : 2.189 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: 0.3256 time to fit residues: 174.9788 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 : 2.333 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096604 restraints weight = 28676.340| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.92 r_work: 0.3028 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- 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 5.99645 ( 1947) SS BOND : bond 0.00178 ( 22) SS BOND : angle 0.98091 ( 44) covalent geometry : bond 0.00332 (20795) covalent geometry : angle 0.53649 (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 : 2.372 Fit side-chains REVERT: H 99 TYR cc_start: 0.8700 (t80) cc_final: 0.8283 (t80) REVERT: B 91 TYR cc_start: 0.7545 (p90) cc_final: 0.7142 (p90) REVERT: C 91 TYR cc_start: 0.8827 (m-80) cc_final: 0.8579 (m-80) REVERT: M 95 ASP cc_start: 0.8395 (t70) cc_final: 0.8089 (t0) REVERT: P 103 LYS cc_start: 0.8612 (tppt) cc_final: 0.8364 (tptt) REVERT: O 100 ASP cc_start: 0.7558 (m-30) cc_final: 0.7312 (m-30) REVERT: T 81 GLU cc_start: 0.7700 (pm20) cc_final: 0.7462 (pm20) REVERT: S 91 TYR cc_start: 0.9045 (m-80) cc_final: 0.8734 (m-10) REVERT: W 72 ASP cc_start: 0.7701 (p0) cc_final: 0.7333 (t0) outliers start: 39 outliers final: 17 residues processed: 360 average time/residue: 0.3218 time to fit residues: 178.6141 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 : 2.151 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 V 79 GLN U 100CASN ** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.090480 restraints weight = 29242.280| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.12 r_work: 0.2912 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.084 20817 Z= 0.393 Angle : 0.700 9.740 28243 Z= 0.375 Chirality : 0.048 0.161 2973 Planarity : 0.005 0.044 3684 Dihedral : 4.785 28.678 2881 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.09 % Allowed : 15.76 % Favored : 81.15 % 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: -0.33 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.05 (0.14), residues: 1210 loop : -0.38 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 103 HIS 0.006 0.001 HIS U 35 PHE 0.026 0.002 PHE Z 96 TYR 0.030 0.003 TYR L 91 ARG 0.007 0.001 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 754) hydrogen bonds : angle 6.10353 ( 1947) SS BOND : bond 0.00411 ( 22) SS BOND : angle 1.78790 ( 44) covalent geometry : bond 0.00951 (20795) covalent geometry : angle 0.69747 (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 371 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 304 time to evaluate : 4.500 Fit side-chains REVERT: H 61 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8422 (t70) REVERT: A 100 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.6835 (t0) REVERT: D 104 VAL cc_start: 0.7707 (t) cc_final: 0.7449 (m) REVERT: C 75 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8226 (mtmt) REVERT: N 103 LYS cc_start: 0.8367 (ttmm) cc_final: 0.8078 (tttp) REVERT: V 17 GLU cc_start: 0.7394 (tt0) cc_final: 0.7114 (tt0) REVERT: X 3 VAL cc_start: 0.9179 (t) cc_final: 0.8959 (m) REVERT: X 17 GLU cc_start: 0.7640 (pt0) cc_final: 0.7372 (pm20) REVERT: Y 56 ASN cc_start: 0.8675 (m-40) cc_final: 0.8357 (m-40) REVERT: Y 98 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8207 (p90) outliers start: 67 outliers final: 45 residues processed: 356 average time/residue: 0.4002 time to fit residues: 222.1131 Evaluate side-chains 341 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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 89 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 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 61 ASP 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 Z residue 77 SER 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 98 PHE 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: 3.9990 chunk 242 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 229 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN D 42 GLN D 92 ASN F 92 ASN Y 76 ASN Y 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095758 restraints weight = 29101.324| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.86 r_work: 0.3007 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20817 Z= 0.124 Angle : 0.513 7.179 28243 Z= 0.274 Chirality : 0.042 0.149 2973 Planarity : 0.004 0.037 3684 Dihedral : 4.126 25.222 2881 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.21 % Allowed : 17.33 % Favored : 80.46 % 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: -0.19 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.15 (0.14), residues: 1210 loop : -0.29 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.006 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 0.03095 ( 754) hydrogen bonds : angle 5.31726 ( 1947) SS BOND : bond 0.00228 ( 22) SS BOND : angle 0.89716 ( 44) covalent geometry : bond 0.00299 (20795) covalent geometry : angle 0.51225 (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 393 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 345 time to evaluate : 2.159 Fit side-chains REVERT: H 61 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8276 (t70) REVERT: H 99 TYR cc_start: 0.8621 (t80) cc_final: 0.8329 (t80) REVERT: B 96 PHE cc_start: 0.8215 (m-80) cc_final: 0.7941 (m-80) REVERT: A 100 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.6824 (t0) REVERT: C 75 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8194 (mtmt) REVERT: F 54 ARG cc_start: 0.8606 (mtm110) cc_final: 0.8200 (ttm-80) REVERT: O 45 LEU cc_start: 0.8718 (mm) cc_final: 0.8301 (mt) REVERT: O 75 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8758 (mtpp) REVERT: Q 82 MET cc_start: 0.9086 (mtt) cc_final: 0.8667 (mtt) REVERT: V 17 GLU cc_start: 0.7340 (tt0) cc_final: 0.7027 (tt0) REVERT: U 100 TYR cc_start: 0.8743 (m-80) cc_final: 0.8541 (m-80) REVERT: X 3 VAL cc_start: 0.9153 (t) cc_final: 0.8937 (m) REVERT: X 17 GLU cc_start: 0.7709 (pt0) cc_final: 0.7494 (pm20) REVERT: W 72 ASP cc_start: 0.7714 (p0) cc_final: 0.7361 (t0) REVERT: Y 98 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8190 (p90) outliers start: 48 outliers final: 33 residues processed: 379 average time/residue: 0.3071 time to fit residues: 178.7378 Evaluate side-chains 366 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 330 time to evaluate : 2.131 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain A residue 100 ASN 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 E residue 78 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 85 GLU 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 U residue 17 SER Chi-restraints excluded: chain X residue 7 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 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 81 GLU Chi-restraints excluded: chain Y residue 5 VAL Chi-restraints excluded: chain Y residue 98 PHE 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: 8.9990 chunk 47 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 243 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 120 optimal weight: 0.0010 chunk 239 optimal weight: 7.9990 chunk 85 optimal weight: 0.1980 chunk 201 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 overall best weight: 3.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100CASN D 42 GLN D 92 ASN U 3 GLN Y 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.092152 restraints weight = 29398.893| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.13 r_work: 0.2944 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20817 Z= 0.234 Angle : 0.577 7.683 28243 Z= 0.306 Chirality : 0.043 0.163 2973 Planarity : 0.004 0.038 3684 Dihedral : 4.316 27.192 2881 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 3.27 % Allowed : 17.51 % Favored : 79.22 % 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: -0.30 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.08 (0.14), residues: 1210 loop : -0.37 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 103 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.002 PHE Z 96 TYR 0.019 0.002 TYR L 91 ARG 0.007 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 754) hydrogen bonds : angle 5.42201 ( 1947) SS BOND : bond 0.00201 ( 22) SS BOND : angle 1.35416 ( 44) covalent geometry : bond 0.00567 (20795) covalent geometry : angle 0.57476 (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 399 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 328 time to evaluate : 2.189 Fit side-chains REVERT: H 61 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8382 (t70) REVERT: H 99 TYR cc_start: 0.8612 (t80) cc_final: 0.8324 (t80) REVERT: B 96 PHE cc_start: 0.8167 (m-80) cc_final: 0.7875 (m-80) REVERT: A 100 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.6727 (t0) REVERT: C 75 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8141 (mtpt) REVERT: O 75 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8753 (mtpp) REVERT: V 4 MET cc_start: 0.8651 (mmm) cc_final: 0.8395 (mmm) REVERT: V 17 GLU cc_start: 0.7447 (tt0) cc_final: 0.7115 (tt0) REVERT: X 3 VAL cc_start: 0.9141 (t) cc_final: 0.8918 (m) REVERT: X 17 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7470 (pm20) REVERT: W 72 ASP cc_start: 0.7714 (p0) cc_final: 0.7356 (t0) REVERT: Z 73 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7329 (tt) REVERT: Y 98 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (p90) outliers start: 71 outliers final: 49 residues processed: 375 average time/residue: 0.3254 time to fit residues: 187.2553 Evaluate side-chains 376 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 63 VAL 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 82 MET 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 28 THR 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 F residue 11 VAL 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 R residue 80 SER Chi-restraints excluded: chain R residue 107 LYS 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 5 THR 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 V residue 85 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 17 GLU 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 21 SER 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 73 LEU 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 53 ASP Chi-restraints excluded: chain Y residue 69 ILE Chi-restraints excluded: chain Y residue 98 PHE Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 41 optimal weight: 0.0670 chunk 173 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 145 optimal weight: 0.0670 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 92 ASN U 3 GLN X 38 GLN Y 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095799 restraints weight = 29092.301| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.15 r_work: 0.2999 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20817 Z= 0.121 Angle : 0.512 8.800 28243 Z= 0.270 Chirality : 0.042 0.154 2973 Planarity : 0.003 0.033 3684 Dihedral : 4.008 24.764 2881 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 2.76 % Allowed : 18.06 % Favored : 79.17 % 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: -0.19 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.15 (0.14), residues: 1210 loop : -0.30 (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 0.014 0.001 TYR U 102 ARG 0.006 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 754) hydrogen bonds : angle 5.08076 ( 1947) SS BOND : bond 0.00137 ( 22) SS BOND : angle 0.93575 ( 44) covalent geometry : bond 0.00291 (20795) covalent geometry : angle 0.51129 (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 404 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 344 time to evaluate : 2.172 Fit side-chains REVERT: H 61 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8322 (t70) REVERT: H 99 TYR cc_start: 0.8614 (t80) cc_final: 0.8266 (t80) REVERT: B 96 PHE cc_start: 0.8145 (m-80) cc_final: 0.7845 (m-80) REVERT: C 75 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8133 (mtmt) REVERT: C 81 GLN cc_start: 0.8384 (tp40) cc_final: 0.8154 (tm-30) REVERT: F 54 ARG cc_start: 0.8636 (mtm110) cc_final: 0.8196 (ttm-80) REVERT: O 75 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8735 (mtpp) REVERT: T 79 GLN cc_start: 0.8912 (mp10) cc_final: 0.7515 (mp10) REVERT: V 17 GLU cc_start: 0.7517 (tt0) cc_final: 0.7172 (tt0) REVERT: U 16 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7734 (mmp80) REVERT: X 17 GLU cc_start: 0.7765 (pt0) cc_final: 0.7400 (pm20) REVERT: X 70 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7220 (pp20) REVERT: W 72 ASP cc_start: 0.7661 (p0) cc_final: 0.7279 (t0) REVERT: W 77 MET cc_start: 0.8818 (ttm) cc_final: 0.8580 (mtp) REVERT: Y 98 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8199 (p90) outliers start: 60 outliers final: 43 residues processed: 381 average time/residue: 0.3059 time to fit residues: 178.3016 Evaluate side-chains 381 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 335 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 D residue 5 THR Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain F residue 11 VAL 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 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 V residue 81 GLU Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 70 GLU 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 13 VAL Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 74 THR 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 98 PHE 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: 9.9990 chunk 50 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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** U 3 GLN Y 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091797 restraints weight = 29378.530| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.14 r_work: 0.2937 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20817 Z= 0.268 Angle : 0.602 11.654 28243 Z= 0.317 Chirality : 0.044 0.170 2973 Planarity : 0.004 0.041 3684 Dihedral : 4.347 27.100 2881 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 3.46 % Allowed : 17.74 % Favored : 78.80 % 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: -0.34 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.06 (0.14), residues: 1210 loop : -0.40 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 103 HIS 0.005 0.001 HIS E 35 PHE 0.019 0.002 PHE Z 96 TYR 0.022 0.002 TYR L 91 ARG 0.007 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 754) hydrogen bonds : angle 5.35088 ( 1947) SS BOND : bond 0.00245 ( 22) SS BOND : angle 1.50461 ( 44) covalent geometry : bond 0.00649 (20795) covalent geometry : angle 0.59911 (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 400 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 325 time to evaluate : 4.988 Fit side-chains revert: symmetry clash REVERT: H 61 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8343 (t70) REVERT: B 96 PHE cc_start: 0.8242 (m-80) cc_final: 0.7939 (m-80) REVERT: A 100 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.6834 (t0) REVERT: D 49 TYR cc_start: 0.8457 (p90) cc_final: 0.8107 (p90) REVERT: D 104 VAL cc_start: 0.7562 (t) cc_final: 0.7316 (m) REVERT: C 75 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8165 (mtmt) REVERT: O 75 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8774 (mtpp) REVERT: Q 82 MET cc_start: 0.9109 (mtt) cc_final: 0.8680 (mtt) REVERT: T 4 MET cc_start: 0.8443 (mmm) cc_final: 0.8199 (mtp) REVERT: T 81 GLU cc_start: 0.8433 (pt0) cc_final: 0.7832 (pm20) REVERT: S 91 TYR cc_start: 0.9128 (m-80) cc_final: 0.8753 (m-10) REVERT: V 4 MET cc_start: 0.8505 (mmm) cc_final: 0.8249 (mmm) REVERT: V 17 GLU cc_start: 0.7440 (tt0) cc_final: 0.7117 (tt0) REVERT: X 17 GLU cc_start: 0.7769 (pt0) cc_final: 0.7417 (pm20) REVERT: X 106 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7090 (t80) REVERT: W 72 ASP cc_start: 0.7681 (p0) cc_final: 0.7376 (t0) REVERT: W 85 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: Z 73 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7336 (tt) REVERT: Y 98 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8251 (p90) outliers start: 75 outliers final: 58 residues processed: 378 average time/residue: 0.4106 time to fit residues: 240.9880 Evaluate side-chains 388 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 324 time to evaluate : 3.548 ------------------------------------------------------------------------------- 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 L residue 106 PHE 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 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 C residue 28 THR 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 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 78 ILE Chi-restraints excluded: chain M residue 75 LYS 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 82 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain Q residue 38 ARG 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 5 THR Chi-restraints excluded: chain T residue 52 SER 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 U residue 17 SER Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 106 PHE 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 85 GLU Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 73 LEU 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 98 PHE 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 ************** Weight determination summary: number of chunks: 250 random chunks: chunk 100 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 223 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 U 3 GLN Y 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094931 restraints weight = 29147.257| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.88 r_work: 0.2999 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20817 Z= 0.125 Angle : 0.515 8.539 28243 Z= 0.271 Chirality : 0.042 0.163 2973 Planarity : 0.003 0.035 3684 Dihedral : 4.034 24.446 2881 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.18 % Favored : 97.78 % Rotamer: Outliers : 2.76 % Allowed : 18.76 % Favored : 78.48 % 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: 0.15 (0.14), residues: 1210 loop : -0.30 (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 0.018 0.001 TYR H 99 ARG 0.007 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 754) hydrogen bonds : angle 5.04142 ( 1947) SS BOND : bond 0.00129 ( 22) SS BOND : angle 0.93752 ( 44) covalent geometry : bond 0.00302 (20795) covalent geometry : angle 0.51407 (28199) *********************** REFINEMENT MACRO_CYCLE 8 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 405 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 345 time to evaluate : 2.655 Fit side-chains revert: symmetry clash REVERT: H 16 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7960 (ttm-80) REVERT: H 61 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8289 (t70) REVERT: H 99 TYR cc_start: 0.8755 (t80) cc_final: 0.8272 (t80) REVERT: B 96 PHE cc_start: 0.8204 (m-80) cc_final: 0.7896 (m-80) REVERT: A 100 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.6838 (t0) REVERT: D 49 TYR cc_start: 0.8353 (p90) cc_final: 0.7977 (p90) REVERT: C 75 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8123 (mtmt) REVERT: F 54 ARG cc_start: 0.8601 (mtm110) cc_final: 0.8214 (ttm-80) REVERT: O 75 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8751 (mtpp) REVERT: O 78 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7989 (tt) REVERT: Q 82 MET cc_start: 0.9089 (mtt) cc_final: 0.8643 (mtt) REVERT: T 4 MET cc_start: 0.8391 (mmm) cc_final: 0.8168 (mtp) REVERT: T 79 GLN cc_start: 0.8809 (mp10) cc_final: 0.8573 (mp10) REVERT: T 81 GLU cc_start: 0.8409 (pt0) cc_final: 0.7846 (pm20) REVERT: S 91 TYR cc_start: 0.9092 (m-80) cc_final: 0.8621 (m-10) REVERT: V 17 GLU cc_start: 0.7379 (tt0) cc_final: 0.7090 (tt0) REVERT: U 16 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7777 (mmp80) REVERT: X 17 GLU cc_start: 0.7778 (pt0) cc_final: 0.7463 (pm20) REVERT: X 106 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6995 (t80) REVERT: W 72 ASP cc_start: 0.7633 (p0) cc_final: 0.7308 (t0) REVERT: Z 54 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7417 (mtm-85) REVERT: Y 98 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8136 (p90) outliers start: 60 outliers final: 50 residues processed: 386 average time/residue: 0.4389 time to fit residues: 263.8305 Evaluate side-chains 384 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 329 time to evaluate : 3.129 ------------------------------------------------------------------------------- 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 78 ILE 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 87 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 LEU 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 75 LYS 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 O residue 82 LEU Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain Q residue 38 ARG 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 5 THR Chi-restraints excluded: chain T residue 52 SER 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 81 GLU Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 106 PHE 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 52 SER 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 84 VAL Chi-restraints excluded: chain Y residue 98 PHE Chi-restraints excluded: chain Y residue 100 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 U 3 GLN Y 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094268 restraints weight = 29233.822| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.02 r_work: 0.2987 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20817 Z= 0.137 Angle : 0.522 6.836 28243 Z= 0.276 Chirality : 0.042 0.157 2973 Planarity : 0.004 0.040 3684 Dihedral : 4.015 24.771 2881 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.64 % Favored : 97.32 % Rotamer: Outliers : 2.95 % Allowed : 19.08 % Favored : 77.97 % 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: -0.15 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.18 (0.14), residues: 1210 loop : -0.27 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 103 HIS 0.006 0.001 HIS E 35 PHE 0.015 0.001 PHE Y 32 TYR 0.018 0.001 TYR U 102 ARG 0.006 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02787 ( 754) hydrogen bonds : angle 4.99542 ( 1947) SS BOND : bond 0.00133 ( 22) SS BOND : angle 1.02332 ( 44) covalent geometry : bond 0.00333 (20795) covalent geometry : angle 0.52096 (28199) *********************** REFINEMENT MACRO_CYCLE 9 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 396 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 332 time to evaluate : 4.715 Fit side-chains revert: symmetry clash REVERT: H 16 ARG cc_start: 0.8303 (ttm-80) cc_final: 0.7959 (ttm-80) REVERT: H 61 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8306 (t70) REVERT: H 99 TYR cc_start: 0.8828 (t80) cc_final: 0.8349 (t80) REVERT: B 96 PHE cc_start: 0.8209 (m-80) cc_final: 0.7946 (m-80) REVERT: A 100 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.6780 (t0) REVERT: A 100 TYR cc_start: 0.8567 (m-80) cc_final: 0.8319 (m-80) REVERT: D 49 TYR cc_start: 0.8334 (p90) cc_final: 0.7930 (p90) REVERT: D 70 GLU cc_start: 0.8254 (tp30) cc_final: 0.7998 (tp30) REVERT: C 75 LYS cc_start: 0.8696 (mtpp) cc_final: 0.8208 (mtmt) REVERT: F 54 ARG cc_start: 0.8628 (mtm110) cc_final: 0.8207 (ttm-80) REVERT: O 75 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8733 (mtpp) REVERT: Q 82 MET cc_start: 0.9123 (mtt) cc_final: 0.8684 (mtt) REVERT: T 79 GLN cc_start: 0.8788 (mp10) cc_final: 0.8513 (mp10) REVERT: T 81 GLU cc_start: 0.8404 (pt0) cc_final: 0.7855 (pm20) REVERT: V 4 MET cc_start: 0.8106 (mmm) cc_final: 0.7754 (mtp) REVERT: V 17 GLU cc_start: 0.7448 (tt0) cc_final: 0.7145 (tt0) REVERT: U 3 GLN cc_start: 0.8655 (tt0) cc_final: 0.8439 (tt0) REVERT: U 16 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7771 (mmp80) REVERT: X 17 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: X 106 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.7001 (t80) REVERT: W 72 ASP cc_start: 0.7631 (p0) cc_final: 0.7280 (t0) REVERT: Z 54 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7433 (mtm-85) REVERT: Y 98 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8196 (p90) outliers start: 64 outliers final: 50 residues processed: 379 average time/residue: 0.5282 time to fit residues: 312.2131 Evaluate side-chains 383 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 328 time to evaluate : 3.998 ------------------------------------------------------------------------------- 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 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 87 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain F residue 10 THR 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 75 LYS 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 82 LEU Chi-restraints excluded: chain R residue 106 PHE Chi-restraints excluded: chain Q residue 38 ARG 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 5 THR Chi-restraints excluded: chain T residue 52 SER 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 81 GLU Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 106 PHE 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 52 SER 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 84 VAL Chi-restraints excluded: chain Y residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 53 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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 Y 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093120 restraints weight = 29240.253| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.15 r_work: 0.2958 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20817 Z= 0.196 Angle : 0.559 8.547 28243 Z= 0.294 Chirality : 0.043 0.156 2973 Planarity : 0.004 0.041 3684 Dihedral : 4.171 25.509 2881 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 2.72 % Allowed : 19.49 % Favored : 77.79 % 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: 0.15 (0.14), residues: 1210 loop : -0.32 (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 E 35 PHE 0.015 0.001 PHE Y 32 TYR 0.023 0.002 TYR U 102 ARG 0.005 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 754) hydrogen bonds : angle 5.11777 ( 1947) SS BOND : bond 0.00183 ( 22) SS BOND : angle 1.22383 ( 44) covalent geometry : bond 0.00475 (20795) covalent geometry : angle 0.55731 (28199) ********************** REFINEMENT MACRO_CYCLE 10 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 388 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 6.223 Fit side-chains revert: symmetry clash REVERT: H 16 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8003 (ttm-80) REVERT: H 61 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8373 (t70) REVERT: H 99 TYR cc_start: 0.8843 (t80) cc_final: 0.8465 (t80) REVERT: B 96 PHE cc_start: 0.8189 (m-80) cc_final: 0.7935 (m-80) REVERT: A 100 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.6790 (t0) REVERT: A 100 TYR cc_start: 0.8592 (m-80) cc_final: 0.8312 (m-80) REVERT: D 49 TYR cc_start: 0.8408 (p90) cc_final: 0.7987 (p90) REVERT: D 104 VAL cc_start: 0.7245 (t) cc_final: 0.7021 (m) REVERT: C 59 TYR cc_start: 0.9150 (m-80) cc_final: 0.8915 (m-80) REVERT: C 75 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8216 (mtmt) REVERT: F 54 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8285 (ttm-80) REVERT: O 75 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8745 (mtpp) REVERT: Q 82 MET cc_start: 0.9150 (mtt) cc_final: 0.8694 (mtt) REVERT: T 81 GLU cc_start: 0.8412 (pt0) cc_final: 0.7861 (pm20) REVERT: S 91 TYR cc_start: 0.9134 (m-80) cc_final: 0.8679 (m-10) REVERT: V 4 MET cc_start: 0.8056 (mmm) cc_final: 0.7805 (mtp) REVERT: V 17 GLU cc_start: 0.7475 (tt0) cc_final: 0.7197 (tt0) REVERT: U 16 ARG cc_start: 0.8108 (tpp80) cc_final: 0.7830 (mmp80) REVERT: X 17 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: X 106 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7021 (t80) REVERT: W 72 ASP cc_start: 0.7645 (p0) cc_final: 0.7304 (t0) REVERT: Y 98 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.8195 (p90) outliers start: 59 outliers final: 51 residues processed: 374 average time/residue: 0.5057 time to fit residues: 295.1482 Evaluate side-chains 383 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 327 time to evaluate : 4.734 ------------------------------------------------------------------------------- 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 78 ILE 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 87 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain F residue 10 THR 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 75 LYS 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 82 LEU Chi-restraints excluded: chain Q residue 38 ARG 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 5 THR Chi-restraints excluded: chain T residue 52 SER 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 U residue 17 SER Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 100 ASN Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 17 GLU Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 76 SER Chi-restraints excluded: chain X residue 92 ASN Chi-restraints excluded: chain X residue 106 PHE 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 52 SER 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 84 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 239 optimal weight: 0.4980 chunk 211 optimal weight: 0.3980 chunk 163 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 111 optimal weight: 0.0370 chunk 11 optimal weight: 4.9990 chunk 238 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.3862 ------------------------------------------------------------------------------- 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 ** Y 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093342 restraints weight = 29251.245| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.14 r_work: 0.2964 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20817 Z= 0.173 Angle : 0.547 6.863 28243 Z= 0.289 Chirality : 0.042 0.155 2973 Planarity : 0.004 0.034 3684 Dihedral : 4.143 25.704 2881 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 3.04 % Allowed : 19.22 % Favored : 77.74 % 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: 0.16 (0.15), residues: 1210 loop : -0.31 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 103 HIS 0.006 0.001 HIS E 35 PHE 0.015 0.001 PHE Y 32 TYR 0.018 0.002 TYR H 99 ARG 0.007 0.000 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 754) hydrogen bonds : angle 5.09446 ( 1947) SS BOND : bond 0.00159 ( 22) SS BOND : angle 1.12061 ( 44) covalent geometry : bond 0.00420 (20795) covalent geometry : angle 0.54594 (28199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13682.41 seconds wall clock time: 248 minutes 57.29 seconds (14937.29 seconds total)