Starting phenix.real_space_refine on Fri Jul 3 14:45:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wci_37440/07_2026/8wci_37440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wci_37440/07_2026/8wci_37440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wci_37440/07_2026/8wci_37440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wci_37440/07_2026/8wci_37440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wci_37440/07_2026/8wci_37440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wci_37440/07_2026/8wci_37440.map" } resolution = 2.2 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 85 5.16 5 Na 9 4.78 5 C 9734 2.51 5 N 2208 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1124 Chain: "B" Number of atoms: 1157 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1112 Chain: "C" Number of atoms: 1149 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1122 Chain: "D" Number of atoms: 1163 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1105 Chain: "E" Number of atoms: 1152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1118 Chain: "F" Number of atoms: 1152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1118 Chain: "G" Number of atoms: 1158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1113 Chain: "H" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain: "I" Number of atoms: 1167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1103 Chain: "J" Number of atoms: 1158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} Conformer: "B" Number of residues, atoms: 156, 1128 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 151} bond proxies already assigned to first conformer: 1113 Chain: "P" Number of atoms: 2685 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 343, 2677 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain breaks: 5 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 343, 2677 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain breaks: 5 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 2727 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 81 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "P" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'W3K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "P" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb=" N AVAL G 13 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL G 13 " occ=0.50 residue: pdb=" N ALEU G 17 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU G 17 " occ=0.50 residue: pdb=" N ATHR G 21 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR G 21 " occ=0.50 residue: pdb=" N ALEU G 75 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU G 75 " occ=0.50 residue: pdb=" N AVAL I 13 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL I 13 " occ=0.50 residue: pdb=" N ALEU I 17 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU I 17 " occ=0.50 residue: pdb=" N ATHR I 21 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR I 21 " occ=0.50 residue: pdb=" N AGLN I 54 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN I 54 " occ=0.50 residue: pdb=" N ALEU I 75 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU I 75 " occ=0.50 residue: pdb=" N AVAL J 13 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL J 13 " occ=0.50 residue: pdb=" N ALEU J 17 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU J 17 " occ=0.50 residue: pdb=" N ATHR J 21 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR J 21 " occ=0.50 ... (remaining 2 not shown) Time building chain proxies: 4.77, per 1000 atoms: 0.32 Number of scatterers: 14876 At special positions: 0 Unit cell: (123.67, 107.07, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 10 15.00 Na 9 11.00 O 2830 8.00 N 2208 7.00 C 9734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.26 Conformation dependent library (CDL) restraints added in 680.8 milliseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3452 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 1 sheets defined 87.8% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 46 removed outlier: 4.325A pdb=" N PHE A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.898A pdb=" N LEU A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 124 Proline residue: A 98 - end of helix removed outlier: 3.926A pdb=" N GLN A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 4.032A pdb=" N GLY A 131 " --> pdb=" O HIS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 156 removed outlier: 4.184A pdb=" N ALA A 142 " --> pdb=" O VAL A 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 11 through 46 removed outlier: 3.655A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 63 through 79 removed outlier: 4.016A pdb=" N LEU B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 124 removed outlier: 3.636A pdb=" N LEU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Proline residue: B 98 - end of helix removed outlier: 3.756A pdb=" N GLN B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.912A pdb=" N GLY B 131 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 156 removed outlier: 4.285A pdb=" N ALA B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 11 through 46 removed outlier: 3.762A pdb=" N SER C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.873A pdb=" N LEU C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 124 Proline residue: C 98 - end of helix removed outlier: 3.721A pdb=" N GLN C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 156 removed outlier: 4.166A pdb=" N GLY C 131 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL C 138 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TYR C 141 " --> pdb=" O MET C 137 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA C 142 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 11 through 46 removed outlier: 3.829A pdb=" N SER D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.820A pdb=" N LEU D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 124 removed outlier: 3.556A pdb=" N LEU D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix removed outlier: 3.867A pdb=" N GLN D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.975A pdb=" N GLY D 131 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 156 removed outlier: 4.123A pdb=" N ALA D 142 " --> pdb=" O VAL D 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 11 through 46 removed outlier: 3.641A pdb=" N SER E 26 " --> pdb=" O ALA E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.888A pdb=" N LEU E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 124 Proline residue: E 98 - end of helix removed outlier: 3.756A pdb=" N GLN E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 4.065A pdb=" N GLY E 131 " --> pdb=" O HIS E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 156 removed outlier: 4.257A pdb=" N ALA E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 11 through 46 removed outlier: 3.680A pdb=" N SER F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 50 removed outlier: 6.464A pdb=" N GLU F 50 " --> pdb=" O SER F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.929A pdb=" N LEU F 67 " --> pdb=" O GLY F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 124 removed outlier: 3.571A pdb=" N LEU F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Proline residue: F 98 - end of helix removed outlier: 3.790A pdb=" N GLN F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.947A pdb=" N GLY F 131 " --> pdb=" O HIS F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 156 removed outlier: 4.227A pdb=" N ALA F 142 " --> pdb=" O VAL F 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 Processing helix chain 'G' and resid 11 through 46 removed outlier: 3.645A pdb=" N SER G 26 " --> pdb=" O ALA G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 51 through 61 Processing helix chain 'G' and resid 63 through 79 removed outlier: 4.005A pdb=" N LEU G 67 " --> pdb=" O GLY G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 124 Proline residue: G 98 - end of helix removed outlier: 3.779A pdb=" N GLN G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.890A pdb=" N GLY G 131 " --> pdb=" O HIS G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 156 removed outlier: 4.267A pdb=" N ALA G 142 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 11 through 46 removed outlier: 3.828A pdb=" N SER H 26 " --> pdb=" O ALA H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 63 through 79 removed outlier: 4.109A pdb=" N LEU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 124 removed outlier: 3.586A pdb=" N LEU H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Proline residue: H 98 - end of helix removed outlier: 3.817A pdb=" N GLN H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.887A pdb=" N GLY H 131 " --> pdb=" O HIS H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 156 removed outlier: 4.187A pdb=" N ALA H 142 " --> pdb=" O VAL H 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 8 Processing helix chain 'I' and resid 11 through 46 removed outlier: 3.707A pdb=" N SER I 26 " --> pdb=" O ALA I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 50 No H-bonds generated for 'chain 'I' and resid 48 through 50' Processing helix chain 'I' and resid 51 through 61 Processing helix chain 'I' and resid 63 through 79 removed outlier: 4.020A pdb=" N LEU I 67 " --> pdb=" O GLY I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 124 Proline residue: I 98 - end of helix removed outlier: 3.741A pdb=" N GLN I 119 " --> pdb=" O ALA I 115 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE I 120 " --> pdb=" O ALA I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 137 removed outlier: 4.214A pdb=" N GLY I 131 " --> pdb=" O HIS I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 156 removed outlier: 4.108A pdb=" N ALA I 142 " --> pdb=" O VAL I 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 8 Processing helix chain 'J' and resid 11 through 46 removed outlier: 3.584A pdb=" N SER J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 50 No H-bonds generated for 'chain 'J' and resid 48 through 50' Processing helix chain 'J' and resid 51 through 61 Processing helix chain 'J' and resid 63 through 78 removed outlier: 3.815A pdb=" N LEU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 124 removed outlier: 3.587A pdb=" N LEU J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) Proline residue: J 98 - end of helix removed outlier: 3.857A pdb=" N GLN J 119 " --> pdb=" O ALA J 115 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE J 120 " --> pdb=" O ALA J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 137 removed outlier: 3.967A pdb=" N GLY J 131 " --> pdb=" O HIS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 156 removed outlier: 4.169A pdb=" N ALA J 142 " --> pdb=" O VAL J 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 29 removed outlier: 4.681A pdb=" N GLN P 23 " --> pdb=" O GLU P 19 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS P 29 " --> pdb=" O VAL P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 48 removed outlier: 4.386A pdb=" N VAL P 46 " --> pdb=" O ASN P 42 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 42 through 48' Processing helix chain 'P' and resid 271 through 281 removed outlier: 4.041A pdb=" N GLU P 278 " --> pdb=" O LEU P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 304 through 315 Processing helix chain 'P' and resid 328 through 334 Processing helix chain 'P' and resid 346 through 348 No H-bonds generated for 'chain 'P' and resid 346 through 348' Processing helix chain 'P' and resid 349 through 357 removed outlier: 3.629A pdb=" N THR P 353 " --> pdb=" O PHE P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 366 through 383 Proline residue: P 372 - end of helix Processing helix chain 'P' and resid 384 through 401 Processing helix chain 'P' and resid 405 through 430 removed outlier: 3.551A pdb=" N ARG P 410 " --> pdb=" O ARG P 406 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE P 411 " --> pdb=" O GLY P 407 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 420 " --> pdb=" O GLU P 416 " (cutoff:3.500A) Proline residue: P 421 - end of helix Processing helix chain 'P' and resid 456 through 483 Processing helix chain 'P' and resid 563 through 571 removed outlier: 3.949A pdb=" N TYR P 571 " --> pdb=" O ASP P 567 " (cutoff:3.500A) Processing helix chain 'P' and resid 572 through 593 Processing helix chain 'P' and resid 596 through 601 removed outlier: 3.743A pdb=" N PHE P 601 " --> pdb=" O PRO P 597 " (cutoff:3.500A) Processing helix chain 'P' and resid 603 through 635 Processing helix chain 'P' and resid 635 through 640 removed outlier: 4.006A pdb=" N PHE P 639 " --> pdb=" O PHE P 635 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 31 through 33 1211 hydrogen bonds defined for protein. 3620 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: 2.43 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2414 1.32 - 1.45: 3589 1.45 - 1.57: 8741 1.57 - 1.70: 20 1.70 - 1.82: 170 Bond restraints: 14934 Sorted by residual: bond pdb=" CAJ W3K P 701 " pdb=" CAK W3K P 701 " ideal model delta sigma weight residual 1.458 1.332 0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" CAA W3K P 701 " pdb=" CAB W3K P 701 " ideal model delta sigma weight residual 1.494 1.389 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CAD W3K P 701 " pdb=" CAH W3K P 701 " ideal model delta sigma weight residual 1.436 1.331 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CAJ W3K P 701 " pdb=" NAI W3K P 701 " ideal model delta sigma weight residual 1.410 1.321 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" CAP W3K P 701 " pdb=" NAQ W3K P 701 " ideal model delta sigma weight residual 1.415 1.330 0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 14929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 19856 2.68 - 5.35: 318 5.35 - 8.03: 38 8.03 - 10.71: 14 10.71 - 13.39: 4 Bond angle restraints: 20230 Sorted by residual: angle pdb=" CA TYR C 141 " pdb=" CB TYR C 141 " pdb=" CG TYR C 141 " ideal model delta sigma weight residual 113.90 104.27 9.63 1.80e+00 3.09e-01 2.86e+01 angle pdb=" CA TYR A 141 " pdb=" CB TYR A 141 " pdb=" CG TYR A 141 " ideal model delta sigma weight residual 113.90 104.29 9.61 1.80e+00 3.09e-01 2.85e+01 angle pdb=" CA TYR D 141 " pdb=" CB TYR D 141 " pdb=" CG TYR D 141 " ideal model delta sigma weight residual 113.90 104.37 9.53 1.80e+00 3.09e-01 2.80e+01 angle pdb=" CA TYR E 141 " pdb=" CB TYR E 141 " pdb=" CG TYR E 141 " ideal model delta sigma weight residual 113.90 104.71 9.19 1.80e+00 3.09e-01 2.61e+01 angle pdb=" CA TYR G 141 " pdb=" CB TYR G 141 " pdb=" CG TYR G 141 " ideal model delta sigma weight residual 113.90 104.73 9.17 1.80e+00 3.09e-01 2.59e+01 ... (remaining 20225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.95: 8497 30.95 - 61.90: 431 61.90 - 92.85: 44 92.85 - 123.80: 0 123.80 - 154.75: 4 Dihedral angle restraints: 8976 sinusoidal: 3505 harmonic: 5471 Sorted by residual: dihedral pdb=" CB5 CDL D 202 " pdb=" CB4 CDL D 202 " pdb=" OB6 CDL D 202 " pdb=" CB6 CDL D 202 " ideal model delta sinusoidal sigma weight residual 144.75 -60.50 -154.75 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CB5 CDL I 201 " pdb=" CB4 CDL I 201 " pdb=" OB6 CDL I 201 " pdb=" CB6 CDL I 201 " ideal model delta sinusoidal sigma weight residual 144.75 -64.21 -151.04 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CB5 CDL F 202 " pdb=" CB4 CDL F 202 " pdb=" OB6 CDL F 202 " pdb=" CB6 CDL F 202 " ideal model delta sinusoidal sigma weight residual 144.75 -65.57 -149.68 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2406 0.149 - 0.298: 12 0.298 - 0.447: 4 0.447 - 0.597: 0 0.597 - 0.746: 3 Chirality restraints: 2425 Sorted by residual: chirality pdb=" CB4 CDL I 201 " pdb=" CB3 CDL I 201 " pdb=" CB6 CDL I 201 " pdb=" OB6 CDL I 201 " both_signs ideal model delta sigma weight residual False -2.61 -1.86 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CB4 CDL H 201 " pdb=" CB3 CDL H 201 " pdb=" CB6 CDL H 201 " pdb=" OB6 CDL H 201 " both_signs ideal model delta sigma weight residual False -2.61 -1.89 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CB4 CDL F 202 " pdb=" CB3 CDL F 202 " pdb=" CB6 CDL F 202 " pdb=" OB6 CDL F 202 " both_signs ideal model delta sigma weight residual False -2.61 -1.96 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 2422 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.054 2.00e-02 2.50e+03 2.94e-02 1.73e+01 pdb=" CG TYR A 141 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 141 " -0.050 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR B 141 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 141 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 141 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 141 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 141 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 141 " 0.047 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR G 141 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR G 141 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR G 141 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR G 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 141 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 141 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR G 141 " 0.015 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1372 2.73 - 3.27: 16317 3.27 - 3.82: 27716 3.82 - 4.36: 34347 4.36 - 4.90: 56078 Nonbonded interactions: 135830 Sorted by model distance: nonbonded pdb=" O HOH E 317 " pdb=" O HOH E 321 " model vdw 2.191 3.040 nonbonded pdb=" O HOH C 215 " pdb=" O HOH C 217 " model vdw 2.201 3.040 nonbonded pdb=" O ALA I 43 " pdb=" OG1 THR I 46 " model vdw 2.201 3.040 nonbonded pdb=" O HOH E 319 " pdb=" O HOH E 321 " model vdw 2.203 3.040 nonbonded pdb=" O GLY F 117 " pdb=" O HOH F 301 " model vdw 2.210 3.040 ... (remaining 135825 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' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'B' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'C' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'D' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'E' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'F' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'G' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'H' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'I' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) selection = (chain 'J' and (resid 1 through 12 or resid 14 through 16 or resid 18 or resid 2 \ 0 or resid 22 through 53 or resid 55 through 56 or resid 58 through 66 or resid \ 68 through 74 or resid 76 through 118 or resid 120 through 156)) } 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=0.50 max=1.00 mean=0.98 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: 8.500 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.270 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.008 0.126 14934 Z= 0.379 Angle : 0.880 13.387 20230 Z= 0.451 Chirality : 0.058 0.746 2425 Planarity : 0.005 0.038 2493 Dihedral : 18.019 154.749 5524 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.62 % Allowed : 17.11 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 1.28 (0.18), residues: 1944 helix: 1.22 (0.12), residues: 1645 sheet: 1.62 (1.19), residues: 22 loop : -1.17 (0.32), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 279 TYR 0.057 0.006 TYR A 141 PHE 0.040 0.004 PHE B 101 TRP 0.007 0.002 TRP P 425 HIS 0.007 0.002 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00832 / 0.38 (14934) covalent geometry : angle 0.88005 / 0.45 (20230) hydrogen bonds : bond 0.09984 / 6.64 ( 1211) hydrogen bonds : angle 5.42196 / 3.97 ( 3620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.520 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 213 average time/residue: 0.7149 time to fit residues: 164.2800 Evaluate side-chains 207 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 323 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN I 88 GLN P 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.095414 restraints weight = 100362.429| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.62 r_work: 0.2950 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14934 Z= 0.145 Angle : 0.567 8.135 20230 Z= 0.304 Chirality : 0.039 0.195 2425 Planarity : 0.003 0.034 2493 Dihedral : 12.784 159.813 2505 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.58 % Allowed : 16.08 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.28 (0.18), residues: 1944 helix: 2.00 (0.12), residues: 1635 sheet: 1.89 (1.15), residues: 22 loop : -1.39 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 645 TYR 0.034 0.003 TYR A 141 PHE 0.020 0.001 PHE C 101 TRP 0.004 0.001 TRP P 298 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (14934) covalent geometry : angle 0.56705 / 0.30 (20230) hydrogen bonds : bond 0.05704 / 3.77 ( 1211) hydrogen bonds : angle 4.68614 / 3.43 ( 3620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.472 Fit side-chains REVERT: B 12 MET cc_start: 0.8289 (tpp) cc_final: 0.7970 (tpp) REVERT: H 126 GLU cc_start: 0.7927 (pm20) cc_final: 0.7727 (pm20) REVERT: P 5 LYS cc_start: 0.7260 (mtmt) cc_final: 0.6913 (mmmt) REVERT: P 39 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.4795 (pp20) REVERT: P 606 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7188 (tp) outliers start: 21 outliers final: 8 residues processed: 243 average time/residue: 0.7010 time to fit residues: 184.7716 Evaluate side-chains 228 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 218 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 305 GLN Chi-restraints excluded: chain P residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 GLN C 48 GLN D 88 GLN F 88 GLN G 8 GLN I 88 GLN P 296 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.095631 restraints weight = 97730.355| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.61 r_work: 0.2958 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14934 Z= 0.140 Angle : 0.547 8.489 20230 Z= 0.293 Chirality : 0.039 0.198 2425 Planarity : 0.003 0.036 2493 Dihedral : 12.405 164.228 2502 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.58 % Allowed : 16.22 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.58 (0.19), residues: 1944 helix: 2.19 (0.12), residues: 1636 sheet: 2.12 (1.11), residues: 22 loop : -1.24 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 18 TYR 0.032 0.003 TYR E 141 PHE 0.020 0.002 PHE C 101 TRP 0.003 0.001 TRP P 369 HIS 0.003 0.001 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (14934) covalent geometry : angle 0.54669 / 0.29 (20230) hydrogen bonds : bond 0.05696 / 3.77 ( 1211) hydrogen bonds : angle 4.56933 / 3.35 ( 3620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 225 time to evaluate : 0.547 Fit side-chains REVERT: B 12 MET cc_start: 0.8286 (tpp) cc_final: 0.7937 (tpp) REVERT: B 124 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8192 (mmmt) REVERT: E 1 MET cc_start: 0.6938 (tpp) cc_final: 0.6504 (tpp) REVERT: P 5 LYS cc_start: 0.7231 (mtmt) cc_final: 0.6887 (mmmt) REVERT: P 39 GLU cc_start: 0.5475 (OUTLIER) cc_final: 0.5140 (tm-30) outliers start: 21 outliers final: 4 residues processed: 237 average time/residue: 0.6780 time to fit residues: 174.1902 Evaluate side-chains 224 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 218 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN G 8 GLN P 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094327 restraints weight = 100020.216| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.62 r_work: 0.2939 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14934 Z= 0.147 Angle : 0.558 8.729 20230 Z= 0.300 Chirality : 0.039 0.210 2425 Planarity : 0.003 0.036 2493 Dihedral : 12.388 169.429 2497 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.65 % Allowed : 16.43 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.58 (0.19), residues: 1944 helix: 2.18 (0.12), residues: 1636 sheet: 2.44 (1.16), residues: 22 loop : -1.20 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 34 TYR 0.036 0.003 TYR A 141 PHE 0.021 0.002 PHE C 101 TRP 0.003 0.001 TRP P 425 HIS 0.003 0.001 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (14934) covalent geometry : angle 0.55802 / 0.30 (20230) hydrogen bonds : bond 0.05900 / 3.90 ( 1211) hydrogen bonds : angle 4.60995 / 3.39 ( 3620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.401 Fit side-chains REVERT: A 12 MET cc_start: 0.8531 (tpp) cc_final: 0.8260 (tpp) REVERT: B 12 MET cc_start: 0.8306 (tpp) cc_final: 0.8010 (tpp) REVERT: B 124 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8191 (mmmt) REVERT: E 1 MET cc_start: 0.6877 (tpp) cc_final: 0.6391 (tpp) REVERT: G 6 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7498 (mp) REVERT: I 79 ASN cc_start: 0.8292 (m-40) cc_final: 0.8054 (m110) REVERT: P 5 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6888 (mmmt) REVERT: P 39 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5097 (tm-30) outliers start: 21 outliers final: 8 residues processed: 232 average time/residue: 0.6746 time to fit residues: 169.6108 Evaluate side-chains 229 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 218 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 170 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 98 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN I 88 GLN P 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.093191 restraints weight = 90780.374| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.56 r_work: 0.2922 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14934 Z= 0.157 Angle : 0.575 9.243 20230 Z= 0.310 Chirality : 0.040 0.218 2425 Planarity : 0.004 0.033 2493 Dihedral : 12.449 178.253 2497 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.99 % Allowed : 16.29 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.55 (0.18), residues: 1944 helix: 2.09 (0.12), residues: 1655 sheet: 2.28 (1.14), residues: 22 loop : -0.89 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 34 TYR 0.038 0.003 TYR A 141 PHE 0.022 0.002 PHE C 101 TRP 0.004 0.001 TRP P 425 HIS 0.003 0.001 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (14934) covalent geometry : angle 0.57518 / 0.31 (20230) hydrogen bonds : bond 0.06200 / 4.10 ( 1211) hydrogen bonds : angle 4.68152 / 3.44 ( 3620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.463 Fit side-chains REVERT: A 12 MET cc_start: 0.8575 (tpp) cc_final: 0.8296 (tpp) REVERT: B 12 MET cc_start: 0.8331 (tpp) cc_final: 0.8023 (tpp) REVERT: B 124 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8243 (mmmt) REVERT: E 1 MET cc_start: 0.6862 (tpp) cc_final: 0.6348 (tpp) REVERT: G 6 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7523 (mp) REVERT: P 5 LYS cc_start: 0.7242 (mtmt) cc_final: 0.6879 (mmmt) REVERT: P 19 GLU cc_start: 0.5277 (mm-30) cc_final: 0.4993 (tp30) REVERT: P 39 GLU cc_start: 0.5469 (OUTLIER) cc_final: 0.5120 (tm-30) outliers start: 26 outliers final: 10 residues processed: 233 average time/residue: 0.6339 time to fit residues: 160.3275 Evaluate side-chains 226 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN I 79 ASN J 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093489 restraints weight = 92669.509| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.53 r_work: 0.2927 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14934 Z= 0.155 Angle : 0.576 9.788 20230 Z= 0.309 Chirality : 0.040 0.222 2425 Planarity : 0.004 0.033 2493 Dihedral : 12.255 161.959 2497 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.58 % Allowed : 17.18 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.54 (0.18), residues: 1944 helix: 2.09 (0.12), residues: 1658 sheet: 2.22 (1.14), residues: 22 loop : -1.01 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 18 TYR 0.039 0.003 TYR E 141 PHE 0.021 0.002 PHE C 101 TRP 0.004 0.001 TRP P 425 HIS 0.003 0.001 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (14934) covalent geometry : angle 0.57583 / 0.31 (20230) hydrogen bonds : bond 0.06128 / 4.05 ( 1211) hydrogen bonds : angle 4.66800 / 3.43 ( 3620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.522 Fit side-chains REVERT: A 12 MET cc_start: 0.8581 (tpp) cc_final: 0.8318 (tpp) REVERT: B 12 MET cc_start: 0.8318 (tpp) cc_final: 0.8000 (tpp) REVERT: B 124 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8242 (mmmt) REVERT: E 1 MET cc_start: 0.6846 (tpp) cc_final: 0.6384 (tpp) REVERT: G 6 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7501 (mp) REVERT: P 5 LYS cc_start: 0.7222 (mtmt) cc_final: 0.6881 (mmmt) REVERT: P 19 GLU cc_start: 0.5202 (mm-30) cc_final: 0.4927 (tp30) REVERT: P 39 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.5066 (tm-30) outliers start: 20 outliers final: 11 residues processed: 229 average time/residue: 0.7165 time to fit residues: 177.7627 Evaluate side-chains 227 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Chi-restraints excluded: chain P residue 355 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 153 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 170 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN I 88 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.095668 restraints weight = 97766.696| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.59 r_work: 0.2959 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14934 Z= 0.139 Angle : 0.545 10.402 20230 Z= 0.292 Chirality : 0.039 0.212 2425 Planarity : 0.003 0.034 2493 Dihedral : 11.989 156.916 2497 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.31 % Allowed : 17.73 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.67 (0.19), residues: 1944 helix: 2.25 (0.12), residues: 1635 sheet: 2.14 (1.14), residues: 22 loop : -1.23 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 279 TYR 0.034 0.003 TYR E 141 PHE 0.018 0.001 PHE C 101 TRP 0.003 0.001 TRP P 425 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (14934) covalent geometry : angle 0.54491 / 0.29 (20230) hydrogen bonds : bond 0.05660 / 3.75 ( 1211) hydrogen bonds : angle 4.53380 / 3.33 ( 3620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.533 Fit side-chains REVERT: A 12 MET cc_start: 0.8541 (tpp) cc_final: 0.8284 (tpp) REVERT: B 12 MET cc_start: 0.8280 (tpp) cc_final: 0.8000 (tpp) REVERT: B 124 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8200 (mmmt) REVERT: E 1 MET cc_start: 0.6679 (tpp) cc_final: 0.6331 (tpp) REVERT: G 6 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7481 (mp) REVERT: P 5 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6894 (mmmt) REVERT: P 19 GLU cc_start: 0.5243 (mm-30) cc_final: 0.4995 (tp30) REVERT: P 39 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.5069 (tm-30) outliers start: 16 outliers final: 10 residues processed: 232 average time/residue: 0.7054 time to fit residues: 177.6698 Evaluate side-chains 230 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 23 GLN Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 147 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN I 79 ASN I 88 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.092782 restraints weight = 94851.090| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.55 r_work: 0.2915 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14934 Z= 0.164 Angle : 0.594 9.356 20230 Z= 0.318 Chirality : 0.040 0.224 2425 Planarity : 0.004 0.033 2493 Dihedral : 12.104 154.558 2497 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 17.66 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.52 (0.18), residues: 1944 helix: 2.08 (0.12), residues: 1658 sheet: 2.11 (1.13), residues: 22 loop : -1.04 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 18 TYR 0.042 0.004 TYR E 141 PHE 0.023 0.002 PHE A 101 TRP 0.004 0.001 TRP P 425 HIS 0.003 0.001 HIS P 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (14934) covalent geometry : angle 0.59354 / 0.32 (20230) hydrogen bonds : bond 0.06309 / 4.17 ( 1211) hydrogen bonds : angle 4.69497 / 3.45 ( 3620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.580 Fit side-chains REVERT: B 12 MET cc_start: 0.8346 (tpp) cc_final: 0.8030 (tpp) REVERT: B 124 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8260 (mmmt) REVERT: E 1 MET cc_start: 0.6681 (tpp) cc_final: 0.6325 (tpp) REVERT: G 6 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7470 (mp) REVERT: H 2 MET cc_start: 0.7264 (tpp) cc_final: 0.7025 (tpt) REVERT: P 5 LYS cc_start: 0.7238 (mtmt) cc_final: 0.6876 (mmmt) REVERT: P 39 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.5066 (tm-30) outliers start: 18 outliers final: 12 residues processed: 225 average time/residue: 0.7389 time to fit residues: 180.0554 Evaluate side-chains 228 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN I 88 GLN J 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093513 restraints weight = 91813.069| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.52 r_work: 0.2923 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14934 Z= 0.157 Angle : 0.589 10.511 20230 Z= 0.314 Chirality : 0.040 0.220 2425 Planarity : 0.004 0.033 2493 Dihedral : 12.063 152.388 2497 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.31 % Allowed : 18.14 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.52 (0.18), residues: 1944 helix: 2.08 (0.12), residues: 1658 sheet: 2.04 (1.12), residues: 22 loop : -1.07 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 279 TYR 0.042 0.003 TYR E 141 PHE 0.021 0.002 PHE C 101 TRP 0.004 0.001 TRP P 425 HIS 0.002 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (14934) covalent geometry : angle 0.58853 / 0.31 (20230) hydrogen bonds : bond 0.06135 / 4.06 ( 1211) hydrogen bonds : angle 4.66250 / 3.43 ( 3620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 0.543 Fit side-chains REVERT: B 12 MET cc_start: 0.8320 (tpp) cc_final: 0.8001 (tpp) REVERT: B 124 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8248 (mmmt) REVERT: E 1 MET cc_start: 0.6738 (tpp) cc_final: 0.6310 (tpp) REVERT: G 1 MET cc_start: 0.5516 (tpp) cc_final: 0.5117 (mtp) REVERT: G 6 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7489 (mp) REVERT: P 5 LYS cc_start: 0.7266 (mtmt) cc_final: 0.6908 (mmmt) REVERT: P 19 GLU cc_start: 0.5305 (mm-30) cc_final: 0.5036 (tp30) REVERT: P 39 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.5064 (tm-30) outliers start: 16 outliers final: 12 residues processed: 224 average time/residue: 0.7564 time to fit residues: 183.4394 Evaluate side-chains 227 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN I 79 ASN I 88 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093676 restraints weight = 85247.440| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.46 r_work: 0.2927 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14934 Z= 0.157 Angle : 0.594 10.771 20230 Z= 0.316 Chirality : 0.040 0.220 2425 Planarity : 0.004 0.033 2493 Dihedral : 12.047 150.029 2497 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.24 % Allowed : 18.28 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.51 (0.18), residues: 1944 helix: 2.08 (0.12), residues: 1658 sheet: 2.04 (1.12), residues: 22 loop : -1.05 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 279 TYR 0.043 0.003 TYR E 141 PHE 0.021 0.002 PHE C 101 TRP 0.004 0.001 TRP P 425 HIS 0.002 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (14934) covalent geometry : angle 0.59404 / 0.32 (20230) hydrogen bonds : bond 0.06135 / 4.06 ( 1211) hydrogen bonds : angle 4.65926 / 3.43 ( 3620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.539 Fit side-chains REVERT: B 12 MET cc_start: 0.8314 (tpp) cc_final: 0.7994 (tpp) REVERT: B 124 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8247 (mmmt) REVERT: E 1 MET cc_start: 0.6673 (tpp) cc_final: 0.6245 (tpp) REVERT: G 1 MET cc_start: 0.5540 (tpp) cc_final: 0.5179 (mtp) REVERT: G 6 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7479 (mp) REVERT: P 5 LYS cc_start: 0.7264 (mtmt) cc_final: 0.6902 (mmmt) REVERT: P 19 GLU cc_start: 0.5311 (mm-30) cc_final: 0.5038 (tp30) REVERT: P 39 GLU cc_start: 0.5450 (OUTLIER) cc_final: 0.5064 (tm-30) REVERT: P 645 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7308 (mtm-85) outliers start: 15 outliers final: 12 residues processed: 222 average time/residue: 0.7453 time to fit residues: 178.9755 Evaluate side-chains 227 residues out of total 1381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 39 GLU Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 305 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 53 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 48 GLN D 88 GLN F 88 GLN I 88 GLN J 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091952 restraints weight = 101059.506| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.61 r_work: 0.2900 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14934 Z= 0.173 Angle : 0.621 10.929 20230 Z= 0.331 Chirality : 0.041 0.225 2425 Planarity : 0.004 0.033 2493 Dihedral : 12.190 148.702 2497 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.17 % Allowed : 18.56 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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 are not related in a simple way. whole: 2.40 (0.18), residues: 1944 helix: 1.99 (0.12), residues: 1658 sheet: 2.08 (1.13), residues: 22 loop : -1.05 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 18 TYR 0.046 0.004 TYR E 141 PHE 0.025 0.002 PHE B 101 TRP 0.005 0.001 TRP P 425 HIS 0.003 0.001 HIS P 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (14934) covalent geometry : angle 0.62065 / 0.33 (20230) hydrogen bonds : bond 0.06511 / 4.31 ( 1211) hydrogen bonds : angle 4.75478 / 3.50 ( 3620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8258.32 seconds wall clock time: 141 minutes 0.49 seconds (8460.49 seconds total)