Starting phenix.real_space_refine on Sun Aug 24 13:06:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dz4_27788/08_2025/8dz4_27788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dz4_27788/08_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_27788/08_2025/8dz4_27788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dz4_27788/08_2025/8dz4_27788.map" model { file = "/net/cci-nas-00/data/ceres_data/8dz4_27788/08_2025/8dz4_27788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dz4_27788/08_2025/8dz4_27788.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.79, per 1000 atoms: 0.24 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: 1.42 Conformation dependent library (CDL) restraints added in 645.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.18 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: 4.19 Time building geometry restraints manager: 2.03 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.570 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- 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 : 6.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG Z 61 TYR 0.020 0.001 TYR O 102 PHE 0.012 0.001 PHE O 27 TRP 0.010 0.001 TRP O 103 HIS 0.008 0.001 HIS A 52A Details of bonding type rmsd covalent geometry : bond 0.00228 (20795) covalent geometry : angle 0.55013 (28199) SS BOND : bond 0.00239 ( 22) SS BOND : angle 0.61189 ( 44) hydrogen bonds : bond 0.24622 ( 754) hydrogen bonds : angle 9.26747 ( 1947) *********************** 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 : 0.781 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: 0.1352 time to fit residues: 72.9461 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 : 0.748 ------------------------------------------------------------------------------- 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 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN A 76 ASN M 81 GLN M 100AHIS O 100AHIS S 100CASN V 1 GLN V 79 GLN U 3 GLN U 100CASN W 100CASN ** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.090730 restraints weight = 29258.420| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.21 r_work: 0.2913 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1621 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= 0.397 Angle : 0.720 10.014 28243 Z= 0.388 Chirality : 0.048 0.164 2973 Planarity : 0.006 0.045 3684 Dihedral : 4.834 28.915 2886 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.41 % Allowed : 15.21 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.10 (0.15), residues: 1155 loop : -0.25 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 83 TYR 0.030 0.003 TYR L 91 PHE 0.028 0.002 PHE Z 96 TRP 0.019 0.003 TRP S 103 HIS 0.005 0.001 HIS A 52A Details of bonding type rmsd covalent geometry : bond 0.00960 (20795) covalent geometry : angle 0.71729 (28199) SS BOND : bond 0.00403 ( 22) SS BOND : angle 1.63094 ( 44) hydrogen bonds : bond 0.04864 ( 754) hydrogen bonds : angle 6.46396 ( 1947) *********************** 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 388 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 314 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: H 61 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8475 (t70) REVERT: B 90 GLN cc_start: 0.6300 (pp30) cc_final: 0.6064 (pp30) REVERT: A 100 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.6728 (t0) REVERT: D 104 VAL cc_start: 0.7633 (t) cc_final: 0.7378 (m) REVERT: C 75 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8594 (mtpp) REVERT: N 103 LYS cc_start: 0.8311 (ttmm) cc_final: 0.8017 (tttp) REVERT: M 95 ASP cc_start: 0.8553 (t70) cc_final: 0.8239 (t0) REVERT: P 45 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.6973 (ttm170) REVERT: T 81 GLU cc_start: 0.7763 (pm20) cc_final: 0.7495 (pm20) REVERT: X 3 VAL cc_start: 0.9213 (t) cc_final: 0.8936 (m) REVERT: Y 34 MET cc_start: 0.9055 (tpp) cc_final: 0.8640 (mmm) outliers start: 74 outliers final: 45 residues processed: 365 average time/residue: 0.1348 time to fit residues: 75.2412 Evaluate side-chains 344 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 296 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS 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 100 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 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 P residue 45 ARG 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 45 LEU Chi-restraints excluded: chain Q residue 55 SER 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 13 VAL Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 89 ILE Chi-restraints excluded: chain U residue 100 ASN 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 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 89 ILE Chi-restraints excluded: chain Y residue 100 HIS Chi-restraints excluded: chain Y residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 179 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN A 76 ASN D 42 GLN D 92 ASN F 92 ASN O 105 GLN Y 76 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 = 0.3635 r_free = 0.3635 target = 0.128261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096488 restraints weight = 28869.906| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.95 r_work: 0.3028 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20817 Z= 0.104 Angle : 0.504 6.916 28243 Z= 0.270 Chirality : 0.042 0.159 2973 Planarity : 0.004 0.038 3684 Dihedral : 4.058 21.471 2881 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.75 % Allowed : 16.91 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.21 (0.14), residues: 1210 loop : -0.22 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 18 TYR 0.013 0.001 TYR H 102 PHE 0.011 0.001 PHE Y 32 TRP 0.009 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00242 (20795) covalent geometry : angle 0.50390 (28199) SS BOND : bond 0.00312 ( 22) SS BOND : angle 0.77101 ( 44) hydrogen bonds : bond 0.03263 ( 754) hydrogen bonds : angle 5.43220 ( 1947) *********************** 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 390 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 352 time to evaluate : 0.627 Fit side-chains REVERT: C 75 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8484 (mtmt) REVERT: M 95 ASP cc_start: 0.8381 (t70) cc_final: 0.8065 (t0) REVERT: O 45 LEU cc_start: 0.8773 (mm) cc_final: 0.8512 (mt) REVERT: T 69 THR cc_start: 0.8433 (p) cc_final: 0.8206 (p) REVERT: T 79 GLN cc_start: 0.8849 (mp10) cc_final: 0.8601 (mp10) REVERT: T 81 GLU cc_start: 0.7702 (pm20) cc_final: 0.7457 (pm20) REVERT: W 40 THR cc_start: 0.7517 (t) cc_final: 0.7301 (p) REVERT: W 72 ASP cc_start: 0.7703 (p0) cc_final: 0.7344 (t0) REVERT: W 99 TYR cc_start: 0.7899 (t80) cc_final: 0.7653 (t80) REVERT: Y 34 MET cc_start: 0.9030 (tpp) cc_final: 0.8824 (mmt) outliers start: 38 outliers final: 19 residues processed: 380 average time/residue: 0.1280 time to fit residues: 76.1590 Evaluate side-chains 347 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 328 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 78 ILE 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 C residue 96 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 40 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 110 THR Chi-restraints excluded: chain Z residue 81 GLU Chi-restraints excluded: chain Y residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 180 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN H 100CASN A 76 ASN D 42 GLN U 100CASN X 38 GLN ** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 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 = 0.3562 r_free = 0.3562 target = 0.122776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.091331 restraints weight = 29491.690| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.11 r_work: 0.2920 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 20817 Z= 0.296 Angle : 0.624 8.936 28243 Z= 0.332 Chirality : 0.045 0.160 2973 Planarity : 0.005 0.039 3684 Dihedral : 4.498 24.281 2881 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.46 % Allowed : 16.59 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.03 (0.14), residues: 1210 loop : -0.41 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 18 TYR 0.027 0.003 TYR H 99 PHE 0.020 0.002 PHE Z 96 TRP 0.015 0.002 TRP S 103 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00719 (20795) covalent geometry : angle 0.62106 (28199) SS BOND : bond 0.00297 ( 22) SS BOND : angle 1.61914 ( 44) hydrogen bonds : bond 0.03638 ( 754) hydrogen bonds : angle 5.67329 ( 1947) *********************** 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 397 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 322 time to evaluate : 0.631 Fit side-chains REVERT: A 100 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.6682 (t0) REVERT: D 49 TYR cc_start: 0.8378 (p90) cc_final: 0.7949 (p90) REVERT: D 104 VAL cc_start: 0.7615 (t) cc_final: 0.7364 (m) REVERT: E 1 GLN cc_start: 0.7800 (mt0) cc_final: 0.7455 (pt0) REVERT: N 103 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8051 (tttp) REVERT: O 100 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8562 (m-40) REVERT: T 81 GLU cc_start: 0.7681 (pm20) cc_final: 0.7427 (pm20) REVERT: V 17 GLU cc_start: 0.7399 (tt0) cc_final: 0.7087 (tt0) REVERT: X 17 GLU cc_start: 0.7765 (pt0) cc_final: 0.7404 (pm20) REVERT: W 72 ASP cc_start: 0.7722 (p0) cc_final: 0.7421 (t0) REVERT: Y 34 MET cc_start: 0.9040 (tpp) cc_final: 0.8829 (mmt) outliers start: 75 outliers final: 48 residues processed: 375 average time/residue: 0.1340 time to fit residues: 77.4110 Evaluate side-chains 362 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 63 VAL Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 81 GLN 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 89 ILE Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain F residue 11 VAL 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 108 LEU Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 78 ILE Chi-restraints excluded: chain Q residue 85 GLU 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 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 74 THR Chi-restraints excluded: chain Z residue 77 SER 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 100 HIS Chi-restraints excluded: chain Y residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 45 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 35 optimal weight: 30.0000 chunk 131 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN B 92 ASN D 42 GLN D 92 ASN U 3 GLN W 100CASN ** W 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 76 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 = 0.3602 r_free = 0.3602 target = 0.125773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.094000 restraints weight = 29104.407| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.96 r_work: 0.2982 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20817 Z= 0.150 Angle : 0.526 7.499 28243 Z= 0.279 Chirality : 0.042 0.154 2973 Planarity : 0.004 0.034 3684 Dihedral : 4.160 20.726 2881 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.00 % Allowed : 17.33 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.06 (0.14), residues: 1210 loop : -0.36 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 18 TYR 0.018 0.002 TYR H 99 PHE 0.014 0.001 PHE B 96 TRP 0.010 0.001 TRP S 103 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00364 (20795) covalent geometry : angle 0.52541 (28199) SS BOND : bond 0.00154 ( 22) SS BOND : angle 0.94945 ( 44) hydrogen bonds : bond 0.03039 ( 754) hydrogen bonds : angle 5.26929 ( 1947) *********************** 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 402 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 337 time to evaluate : 0.542 Fit side-chains REVERT: H 61 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8323 (t70) REVERT: H 99 TYR cc_start: 0.8758 (t80) cc_final: 0.8405 (t80) REVERT: C 75 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8398 (mtmt) REVERT: F 54 ARG cc_start: 0.8583 (mtm110) cc_final: 0.8169 (ttm-80) REVERT: O 45 LEU cc_start: 0.8718 (mm) cc_final: 0.8416 (mt) REVERT: O 75 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8520 (mtmt) REVERT: O 100 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8585 (m-40) REVERT: V 17 GLU cc_start: 0.7378 (tt0) cc_final: 0.7072 (tt0) REVERT: X 17 GLU cc_start: 0.7624 (pt0) cc_final: 0.7346 (pm20) REVERT: X 70 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7282 (pp20) REVERT: X 106 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7195 (t80) REVERT: W 72 ASP cc_start: 0.7681 (p0) cc_final: 0.7364 (t0) REVERT: W 85 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: Y 34 MET cc_start: 0.9032 (tpp) cc_final: 0.8793 (mmt) outliers start: 65 outliers final: 42 residues processed: 381 average time/residue: 0.1375 time to fit residues: 81.1296 Evaluate side-chains 375 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 89 ILE Chi-restraints excluded: chain C residue 96 SER 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 11 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 78 ILE Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 100 ASN Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 85 GLU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 78 ILE Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 70 GLU 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 100 ASN 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 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 84 VAL Chi-restraints excluded: chain Y residue 100 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 55 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 83 optimal weight: 0.2980 chunk 160 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 112 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 179 optimal weight: 0.0970 overall best weight: 0.4960 ------------------------------------------------------------------------------- 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 W 100CASN 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 = 0.3640 r_free = 0.3640 target = 0.128816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098144 restraints weight = 28827.241| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.85 r_work: 0.3044 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20817 Z= 0.088 Angle : 0.488 6.346 28243 Z= 0.258 Chirality : 0.041 0.159 2973 Planarity : 0.003 0.031 3684 Dihedral : 3.831 17.048 2881 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.94 % Favored : 98.02 % Rotamer: Outliers : 1.98 % Allowed : 18.48 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.26 (0.14), residues: 1199 loop : -0.30 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 18 TYR 0.015 0.001 TYR U 102 PHE 0.014 0.001 PHE Y 32 TRP 0.009 0.001 TRP M 103 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00202 (20795) covalent geometry : angle 0.48741 (28199) SS BOND : bond 0.00185 ( 22) SS BOND : angle 0.81338 ( 44) hydrogen bonds : bond 0.02654 ( 754) hydrogen bonds : angle 4.91207 ( 1947) *********************** 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 393 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 0.617 Fit side-chains REVERT: H 61 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8199 (t70) REVERT: H 99 TYR cc_start: 0.8637 (t80) cc_final: 0.8267 (t80) REVERT: A 100 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.6832 (t0) REVERT: C 46 GLU cc_start: 0.8257 (tt0) cc_final: 0.7938 (pt0) REVERT: C 75 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8492 (mtmt) REVERT: C 81 GLN cc_start: 0.8344 (tp40) cc_final: 0.8011 (tm-30) REVERT: F 54 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8170 (ttm-80) REVERT: R 42 GLN cc_start: 0.8621 (mt0) cc_final: 0.8359 (mt0) REVERT: T 79 GLN cc_start: 0.8859 (mp10) cc_final: 0.7629 (mp10) REVERT: S 91 TYR cc_start: 0.9062 (m-80) cc_final: 0.8581 (m-10) REVERT: V 17 GLU cc_start: 0.7462 (tt0) cc_final: 0.7141 (tt0) REVERT: U 16 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7817 (mmp80) REVERT: X 106 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7102 (t80) REVERT: W 72 ASP cc_start: 0.7643 (p0) cc_final: 0.7307 (t0) REVERT: W 99 TYR cc_start: 0.8090 (t80) cc_final: 0.7648 (t80) REVERT: Z 54 ARG cc_start: 0.7945 (mtp-110) cc_final: 0.7301 (ttm110) REVERT: Y 34 MET cc_start: 0.8992 (tpp) cc_final: 0.7854 (mmp) outliers start: 43 outliers final: 33 residues processed: 380 average time/residue: 0.1435 time to fit residues: 83.6844 Evaluate side-chains 370 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain C residue 28 THR 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 11 VAL Chi-restraints excluded: chain E residue 78 ILE 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 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 78 LEU Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain X residue 20 THR Chi-restraints excluded: chain X residue 106 PHE Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain W residue 100 ASN 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 81 GLU Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 84 VAL 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 5 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN B 92 ASN D 42 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 GLN O 3 GLN U 3 GLN ** 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 = 0.3605 r_free = 0.3605 target = 0.125968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.093970 restraints weight = 29036.341| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.00 r_work: 0.2980 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20817 Z= 0.173 Angle : 0.540 8.719 28243 Z= 0.284 Chirality : 0.042 0.164 2973 Planarity : 0.004 0.035 3684 Dihedral : 4.028 18.658 2881 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.72 % Allowed : 18.39 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.17 (0.14), residues: 1210 loop : -0.26 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 18 TYR 0.021 0.002 TYR B 91 PHE 0.015 0.001 PHE Y 32 TRP 0.011 0.001 TRP S 103 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00423 (20795) covalent geometry : angle 0.53788 (28199) SS BOND : bond 0.00163 ( 22) SS BOND : angle 1.24179 ( 44) hydrogen bonds : bond 0.02923 ( 754) hydrogen bonds : angle 5.02611 ( 1947) *********************** 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 391 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 332 time to evaluate : 0.796 Fit side-chains REVERT: H 61 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8335 (t70) REVERT: B 91 TYR cc_start: 0.7800 (p90) cc_final: 0.7388 (p90) REVERT: A 100 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.6795 (t0) REVERT: D 49 TYR cc_start: 0.8281 (p90) cc_final: 0.7904 (p90) REVERT: F 11 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7573 (p) REVERT: F 54 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8191 (ttm-80) REVERT: E 43 LYS cc_start: 0.7038 (ptpp) cc_final: 0.6346 (mttt) REVERT: O 100 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8590 (m-40) REVERT: T 79 GLN cc_start: 0.8862 (mp10) cc_final: 0.8434 (mp10) REVERT: S 91 TYR cc_start: 0.9128 (m-80) cc_final: 0.8682 (m-10) REVERT: V 17 GLU cc_start: 0.7433 (tt0) cc_final: 0.7091 (tt0) REVERT: U 16 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7821 (mmp80) REVERT: X 106 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7054 (t80) REVERT: W 72 ASP cc_start: 0.7666 (p0) cc_final: 0.7318 (t0) REVERT: W 85 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: Y 34 MET cc_start: 0.9006 (tpp) cc_final: 0.7849 (mmp) outliers start: 59 outliers final: 45 residues processed: 371 average time/residue: 0.1551 time to fit residues: 88.3007 Evaluate side-chains 379 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 THR 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 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 82 MET Chi-restraints excluded: chain C residue 89 ILE 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 75 LYS 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 P residue 85 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 100 ASN 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 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 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 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 85 GLU Chi-restraints excluded: chain W residue 110 THR 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 84 VAL Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Y residue 100 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 45 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 P 42 GLN O 3 GLN W 100CASN Y 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092755 restraints weight = 29283.628| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.13 r_work: 0.2949 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20817 Z= 0.222 Angle : 0.576 8.065 28243 Z= 0.303 Chirality : 0.043 0.166 2973 Planarity : 0.004 0.033 3684 Dihedral : 4.238 20.109 2881 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.23 % Allowed : 18.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2572 helix: None (None), residues: 0 sheet: 0.16 (0.15), residues: 1155 loop : -0.31 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 18 TYR 0.025 0.002 TYR H 99 PHE 0.016 0.001 PHE Y 32 TRP 0.011 0.002 TRP S 103 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00538 (20795) covalent geometry : angle 0.57387 (28199) SS BOND : bond 0.00218 ( 22) SS BOND : angle 1.28548 ( 44) hydrogen bonds : bond 0.03082 ( 754) hydrogen bonds : angle 5.21621 ( 1947) *********************** 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 400 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 330 time to evaluate : 0.835 Fit side-chains REVERT: L 54 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.8581 (mtm110) REVERT: H 61 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8388 (t70) REVERT: B 91 TYR cc_start: 0.7821 (p90) cc_final: 0.7393 (p90) REVERT: A 100 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.6775 (t0) REVERT: D 49 TYR cc_start: 0.8392 (p90) cc_final: 0.8027 (p90) REVERT: D 104 VAL cc_start: 0.7278 (t) cc_final: 0.7049 (m) REVERT: C 75 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8543 (mtmt) REVERT: C 81 GLN cc_start: 0.8431 (tp40) cc_final: 0.7934 (tm-30) REVERT: F 11 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7591 (p) REVERT: F 54 ARG cc_start: 0.8658 (mtm110) cc_final: 0.8192 (ttm-80) REVERT: E 43 LYS cc_start: 0.7099 (ptpp) cc_final: 0.6613 (mttt) REVERT: M 3 GLN cc_start: 0.8549 (tp40) cc_final: 0.8286 (mm-40) REVERT: O 100 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8606 (m-40) REVERT: T 79 GLN cc_start: 0.8846 (mp10) cc_final: 0.8308 (mp10) REVERT: S 91 TYR cc_start: 0.9145 (m-80) cc_final: 0.8731 (m-10) REVERT: V 17 GLU cc_start: 0.7451 (tt0) cc_final: 0.7180 (tt0) REVERT: X 106 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7123 (t80) REVERT: W 72 ASP cc_start: 0.7669 (p0) cc_final: 0.7337 (t0) REVERT: W 85 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: Y 34 MET cc_start: 0.9058 (tpp) cc_final: 0.8809 (mmt) outliers start: 70 outliers final: 57 residues processed: 376 average time/residue: 0.1505 time to fit residues: 87.5058 Evaluate side-chains 389 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 78 ILE 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 D residue 92 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 96 SER 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 75 LYS 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 P residue 85 VAL Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 100 ASN 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 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 3 VAL 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 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 40 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 100 ASN Chi-restraints excluded: chain W residue 110 THR 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 84 VAL Chi-restraints excluded: chain Y residue 89 ILE 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 156 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 O 3 GLN U 3 GLN W 100CASN Y 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094644 restraints weight = 29033.383| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.12 r_work: 0.2984 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20817 Z= 0.132 Angle : 0.525 8.343 28243 Z= 0.276 Chirality : 0.042 0.156 2973 Planarity : 0.003 0.031 3684 Dihedral : 4.054 18.484 2881 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.74 % Rotamer: Outliers : 3.13 % Allowed : 18.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2572 helix: None (None), residues: 0 sheet: 0.19 (0.15), residues: 1155 loop : -0.27 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 94 TYR 0.019 0.002 TYR H 99 PHE 0.015 0.001 PHE Y 32 TRP 0.009 0.001 TRP M 103 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00320 (20795) covalent geometry : angle 0.52453 (28199) SS BOND : bond 0.00130 ( 22) SS BOND : angle 0.94725 ( 44) hydrogen bonds : bond 0.02788 ( 754) hydrogen bonds : angle 5.03197 ( 1947) *********************** 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 398 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 330 time to evaluate : 0.817 Fit side-chains REVERT: L 54 ARG cc_start: 0.8922 (mtm-85) cc_final: 0.8526 (mtm110) REVERT: H 61 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8331 (t70) REVERT: B 91 TYR cc_start: 0.7851 (p90) cc_final: 0.7434 (p90) REVERT: A 100 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.6878 (t0) REVERT: A 100 TYR cc_start: 0.8568 (m-80) cc_final: 0.8294 (m-80) REVERT: D 49 TYR cc_start: 0.8407 (p90) cc_final: 0.8030 (p90) REVERT: C 75 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8564 (mtmt) REVERT: C 81 GLN cc_start: 0.8414 (tp40) cc_final: 0.7985 (tm-30) REVERT: F 11 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7656 (p) REVERT: F 54 ARG cc_start: 0.8630 (mtm110) cc_final: 0.8210 (ttm-80) REVERT: E 43 LYS cc_start: 0.6829 (ptpp) cc_final: 0.6355 (mttt) REVERT: O 100 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8597 (m-40) REVERT: T 79 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: T 81 GLU cc_start: 0.8362 (pt0) cc_final: 0.7827 (pm20) REVERT: S 91 TYR cc_start: 0.9114 (m-80) cc_final: 0.8649 (m-10) REVERT: V 17 GLU cc_start: 0.7424 (tt0) cc_final: 0.7149 (tt0) REVERT: U 16 ARG cc_start: 0.8104 (tpp80) cc_final: 0.7841 (mmp80) REVERT: X 106 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7096 (t80) REVERT: W 72 ASP cc_start: 0.7602 (p0) cc_final: 0.7326 (t0) REVERT: W 85 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: Y 34 MET cc_start: 0.9055 (tpp) cc_final: 0.8807 (mmt) outliers start: 68 outliers final: 49 residues processed: 377 average time/residue: 0.1576 time to fit residues: 90.8914 Evaluate side-chains 378 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 322 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 78 ILE 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 11 VAL 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 89 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 O residue 100 ASN 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 5 THR Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 GLN 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 81 GLU Chi-restraints excluded: chain U residue 28 THR 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 100 ASN Chi-restraints excluded: chain W residue 110 THR Chi-restraints excluded: chain Z residue 52 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 100 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 85 optimal weight: 0.0010 chunk 189 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 228 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- 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 O 3 GLN O 81 GLN W 100CASN Y 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093186 restraints weight = 29298.667| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.13 r_work: 0.2949 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20817 Z= 0.207 Angle : 0.570 7.823 28243 Z= 0.300 Chirality : 0.043 0.158 2973 Planarity : 0.004 0.033 3684 Dihedral : 4.203 18.993 2881 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 3.27 % Allowed : 18.43 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2572 helix: None (None), residues: 0 sheet: 0.14 (0.15), residues: 1155 loop : -0.32 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 24 TYR 0.033 0.002 TYR O 102 PHE 0.016 0.001 PHE Y 32 TRP 0.011 0.001 TRP S 103 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00502 (20795) covalent geometry : angle 0.56798 (28199) SS BOND : bond 0.00200 ( 22) SS BOND : angle 1.22991 ( 44) hydrogen bonds : bond 0.03014 ( 754) hydrogen bonds : angle 5.15941 ( 1947) ********************** 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 397 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 326 time to evaluate : 0.818 Fit side-chains REVERT: L 54 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.8565 (mtm110) REVERT: H 61 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8348 (t70) REVERT: A 100 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6890 (t0) REVERT: D 49 TYR cc_start: 0.8487 (p90) cc_final: 0.8092 (p90) REVERT: D 70 GLU cc_start: 0.8307 (tp30) cc_final: 0.8063 (tp30) REVERT: D 104 VAL cc_start: 0.7231 (t) cc_final: 0.6990 (m) REVERT: C 75 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8558 (mtmt) REVERT: F 11 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7662 (p) REVERT: F 54 ARG cc_start: 0.8645 (mtm110) cc_final: 0.8137 (mtm-85) REVERT: E 43 LYS cc_start: 0.6978 (ptpp) cc_final: 0.6539 (mttt) REVERT: M 3 GLN cc_start: 0.8561 (tp40) cc_final: 0.8305 (mm-40) REVERT: O 75 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8668 (mtmm) REVERT: O 100 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8607 (m-40) REVERT: T 79 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: T 81 GLU cc_start: 0.8408 (pt0) cc_final: 0.7866 (pm20) REVERT: S 91 TYR cc_start: 0.9133 (m-80) cc_final: 0.8701 (m-10) REVERT: V 17 GLU cc_start: 0.7438 (tt0) cc_final: 0.7166 (tt0) REVERT: X 106 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7086 (t80) REVERT: W 72 ASP cc_start: 0.7660 (p0) cc_final: 0.7358 (t0) REVERT: W 85 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: Y 34 MET cc_start: 0.9093 (tpp) cc_final: 0.8859 (mmt) outliers start: 71 outliers final: 58 residues processed: 378 average time/residue: 0.1412 time to fit residues: 82.4990 Evaluate side-chains 390 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 78 ILE 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 82 MET 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 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 89 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 O residue 100 ASN 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 5 THR Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 GLN 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 81 GLU Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain X residue 5 THR 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 100 ASN Chi-restraints excluded: chain W residue 110 THR 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 100 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 133 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 206 optimal weight: 0.1980 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN D 92 ASN W 100CASN Y 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093087 restraints weight = 29527.952| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.10 r_work: 0.2943 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20817 Z= 0.209 Angle : 0.573 8.382 28243 Z= 0.301 Chirality : 0.043 0.158 2973 Planarity : 0.004 0.033 3684 Dihedral : 4.237 19.171 2881 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 3.27 % Allowed : 18.34 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.17), residues: 2572 helix: None (None), residues: 0 sheet: 0.12 (0.15), residues: 1155 loop : -0.34 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 18 TYR 0.031 0.002 TYR O 102 PHE 0.016 0.001 PHE Y 32 TRP 0.011 0.001 TRP S 103 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00507 (20795) covalent geometry : angle 0.57157 (28199) SS BOND : bond 0.00197 ( 22) SS BOND : angle 1.18745 ( 44) hydrogen bonds : bond 0.03009 ( 754) hydrogen bonds : angle 5.18563 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5099.45 seconds wall clock time: 88 minutes 12.78 seconds (5292.78 seconds total)