Starting phenix.real_space_refine on Thu Sep 18 08:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w20_43736/09_2025/8w20_43736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w20_43736/09_2025/8w20_43736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w20_43736/09_2025/8w20_43736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w20_43736/09_2025/8w20_43736.map" model { file = "/net/cci-nas-00/data/ceres_data/8w20_43736/09_2025/8w20_43736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w20_43736/09_2025/8w20_43736.cif" } resolution = 4.3 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= 0.110 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 9462 2.51 5 N 3000 2.21 5 O 2900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15412 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 768 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2091 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 280} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1275 Unresolved non-hydrogen dihedrals: 781 Unresolved non-hydrogen chiralities: 114 Planarities with less than four sites: {'ASP:plan': 37, 'ARG:plan': 20, 'GLN:plan1': 13, 'ASN:plan1': 19, 'TYR:plan': 9, 'GLU:plan': 7, 'HIS:plan': 5, 'PHE:plan': 8, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 547 Chain: "A" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 4279 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 15, 'TRANS': 716} Chain breaks: 1 Unresolved non-hydrogen bonds: 1073 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'ASP:plan': 53, 'GLU:plan': 52, 'ARG:plan': 25, 'TYR:plan': 4, 'ASN:plan1': 13, 'GLN:plan1': 21, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 672 Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 756 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1125 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 12, 'TRANS': 208} Unresolved non-hydrogen bonds: 497 Unresolved non-hydrogen angles: 649 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASP:plan': 21, 'PHE:plan': 5, 'ARG:plan': 12, 'TYR:plan': 3, 'GLN:plan1': 9, 'TRP:plan': 1, 'ASN:plan1': 8, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 278 Chain: "F" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 696 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ASP:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "G" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1115 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 641 Unresolved non-hydrogen dihedrals: 373 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'ASP:plan': 20, 'PHE:plan': 5, 'ARG:plan': 12, 'TYR:plan': 3, 'GLN:plan1': 9, 'TRP:plan': 1, 'ASN:plan1': 8, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 275 Chain: "H" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 728 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 2044 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PTRANS': 17, 'TRANS': 387} Chain breaks: 12 Unresolved non-hydrogen bonds: 1029 Unresolved non-hydrogen angles: 1346 Unresolved non-hydrogen dihedrals: 829 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'ASP:plan': 37, 'PHE:plan': 9, 'ARG:plan': 20, 'TYR:plan': 11, 'GLN:plan1': 13, 'TRP:plan': 8, 'ASN:plan1': 19, 'GLU:plan': 8, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 580 Chain: "J" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 698 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASP:plan': 8, 'ARG:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 99 Chain: "K" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1112 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 12, 'TRANS': 206} Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'ASP:plan': 20, 'PHE:plan': 5, 'ARG:plan': 12, 'TYR:plan': 3, 'GLN:plan1': 9, 'TRP:plan': 1, 'ASN:plan1': 8, 'GLU:plan': 5, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 275 Time building chain proxies: 4.34, per 1000 atoms: 0.28 Number of scatterers: 15412 At special positions: 0 Unit cell: (236.04, 239.412, 210.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2900 8.00 N 3000 7.00 C 9462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 71 " distance=2.11 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 222 " distance=2.03 Simple disulfide: pdb=" SG CYS D 78 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 71 " distance=2.10 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 78 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 71 " distance=2.09 Simple disulfide: pdb=" SG CYS G 192 " - pdb=" SG CYS G 222 " distance=2.03 Simple disulfide: pdb=" SG CYS H 78 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 71 " distance=2.08 Simple disulfide: pdb=" SG CYS I 192 " - pdb=" SG CYS I 222 " distance=2.03 Simple disulfide: pdb=" SG CYS J 78 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 71 " distance=2.07 Simple disulfide: pdb=" SG CYS K 192 " - pdb=" SG CYS K 222 " distance=2.02 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: 1.32 Conformation dependent library (CDL) restraints added in 936.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 31 sheets defined 30.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 54 through 62 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 81 through 111 Proline residue: A 93 - end of helix removed outlier: 4.055A pdb=" N HIS A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 Processing helix chain 'A' and resid 126 through 136 Processing helix chain 'A' and resid 138 through 157 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 182 through 203 removed outlier: 3.571A pdb=" N THR A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 228 through 335 Processing helix chain 'A' and resid 445 through 595 removed outlier: 3.716A pdb=" N THR A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN A 514 " --> pdb=" O THR A 510 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 618 removed outlier: 3.817A pdb=" N LYS A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 631 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 643 through 664 removed outlier: 3.863A pdb=" N THR A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 690 through 696 Processing helix chain 'A' and resid 696 through 709 removed outlier: 3.505A pdb=" N VAL A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 Processing helix chain 'A' and resid 727 through 737 Processing helix chain 'A' and resid 737 through 758 removed outlier: 3.511A pdb=" N GLY A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 Processing helix chain 'A' and resid 773 through 783 Processing helix chain 'A' and resid 783 through 889 Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.551A pdb=" N ALA D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 151 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.533A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 151 Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'H' and resid 54 through 62 removed outlier: 3.538A pdb=" N ALA H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 151 Processing helix chain 'I' and resid 69 through 73 Processing helix chain 'I' and resid 238 through 247 Processing helix chain 'J' and resid 54 through 62 Processing helix chain 'J' and resid 148 through 151 Processing helix chain 'K' and resid 69 through 73 Processing helix chain 'K' and resid 238 through 247 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.781A pdb=" N CYS B 96 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106 removed outlier: 3.508A pdb=" N ALA B 104 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR B 126 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU B 162 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 124 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.535A pdb=" N GLU C 112 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N THR C 91 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 7.310A pdb=" N ARG C 137 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY C 212 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 233 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER C 217 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASP C 231 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL C 176 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN C 182 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASP C 203 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL C 152 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 212 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN C 202 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 210 " --> pdb=" O GLN C 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS C 204 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AA6, first strand: chain 'C' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'C' and resid 369 through 369 Processing sheet with id=AA8, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.607A pdb=" N THR C 411 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N THR C 425 " --> pdb=" O THR C 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 485 through 486 Processing sheet with id=AB1, first strand: chain 'D' and resid 73 through 76 removed outlier: 3.609A pdb=" N CYS D 96 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 106 removed outlier: 6.755A pdb=" N THR D 126 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU D 162 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS D 124 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 43 through 48 removed outlier: 3.511A pdb=" N GLU E 112 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR E 91 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 137 through 138 removed outlier: 7.325A pdb=" N ARG E 137 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLY E 212 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE E 233 " --> pdb=" O ASN E 215 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER E 217 " --> pdb=" O ASP E 231 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP E 231 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA E 180 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL E 176 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN E 182 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASP E 203 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL E 152 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 212 " --> pdb=" O LEU E 200 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN E 202 " --> pdb=" O LEU E 210 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU E 210 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS E 204 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU E 208 " --> pdb=" O LYS E 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 73 through 76 removed outlier: 3.718A pdb=" N CYS F 96 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN F 85 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE F 116 " --> pdb=" O GLN F 85 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET F 87 " --> pdb=" O TYR F 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.717A pdb=" N THR F 126 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU F 162 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS F 124 " --> pdb=" O LEU F 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 43 through 48 removed outlier: 3.517A pdb=" N GLU G 112 " --> pdb=" O ARG G 125 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR G 91 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 137 through 138 removed outlier: 7.317A pdb=" N ARG G 137 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY G 212 " --> pdb=" O ARG G 137 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE G 233 " --> pdb=" O ASN G 215 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER G 217 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP G 231 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ALA G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL G 176 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN G 182 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP G 203 " --> pdb=" O PRO G 148 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL G 152 " --> pdb=" O PRO G 199 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU G 200 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 73 through 76 removed outlier: 3.664A pdb=" N CYS H 96 " --> pdb=" O THR H 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 104 through 106 removed outlier: 3.525A pdb=" N ALA H 104 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR H 126 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU H 162 " --> pdb=" O LYS H 124 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS H 124 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 33 through 34 removed outlier: 3.789A pdb=" N ASP I 33 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP I 203 " --> pdb=" O PRO I 148 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL I 152 " --> pdb=" O PRO I 199 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 200 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG I 137 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY I 212 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 33 through 34 removed outlier: 3.789A pdb=" N ASP I 33 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN I 182 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL I 176 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA I 180 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASP I 231 " --> pdb=" O SER I 217 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N SER I 217 " --> pdb=" O ASP I 231 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE I 233 " --> pdb=" O ASN I 215 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ARG I 137 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLY I 212 " --> pdb=" O ARG I 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 43 through 48 removed outlier: 3.515A pdb=" N GLU I 112 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR I 91 " --> pdb=" O VAL I 110 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 259 through 262 Processing sheet with id=AC6, first strand: chain 'I' and resid 333 through 334 Processing sheet with id=AC7, first strand: chain 'I' and resid 369 through 369 Processing sheet with id=AC8, first strand: chain 'I' and resid 409 through 413 removed outlier: 3.590A pdb=" N THR I 411 " --> pdb=" O THR I 425 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR I 425 " --> pdb=" O THR I 411 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 485 through 486 Processing sheet with id=AD1, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.608A pdb=" N CYS J 96 " --> pdb=" O THR J 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 104 through 106 removed outlier: 6.721A pdb=" N THR J 126 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU J 162 " --> pdb=" O LYS J 124 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS J 124 " --> pdb=" O LEU J 162 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 43 through 48 removed outlier: 3.532A pdb=" N GLU K 112 " --> pdb=" O ARG K 125 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N THR K 91 " --> pdb=" O VAL K 110 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 137 through 138 removed outlier: 7.333A pdb=" N ARG K 137 " --> pdb=" O LEU K 210 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N GLY K 212 " --> pdb=" O ARG K 137 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE K 233 " --> pdb=" O ASN K 215 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER K 217 " --> pdb=" O ASP K 231 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP K 231 " --> pdb=" O SER K 217 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA K 180 " --> pdb=" O VAL K 176 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL K 176 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASN K 182 " --> pdb=" O THR K 174 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP K 203 " --> pdb=" O PRO K 148 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL K 152 " --> pdb=" O PRO K 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU K 200 " --> pdb=" O VAL K 211 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3021 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2867 1.26 - 1.40: 3476 1.40 - 1.55: 9101 1.55 - 1.69: 80 1.69 - 1.83: 70 Bond restraints: 15594 Sorted by residual: bond pdb=" C LYS B 102 " pdb=" O LYS B 102 " ideal model delta sigma weight residual 1.235 1.121 0.114 1.30e-02 5.92e+03 7.73e+01 bond pdb=" CA ARG A 234 " pdb=" C ARG A 234 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.26e-02 6.30e+03 5.41e+01 bond pdb=" C LYS D 124 " pdb=" O LYS D 124 " ideal model delta sigma weight residual 1.236 1.169 0.066 1.21e-02 6.83e+03 3.01e+01 bond pdb=" N ASP A 599 " pdb=" CA ASP A 599 " ideal model delta sigma weight residual 1.457 1.491 -0.035 6.40e-03 2.44e+04 2.94e+01 bond pdb=" CA LEU A 638 " pdb=" C LEU A 638 " ideal model delta sigma weight residual 1.524 1.592 -0.068 1.28e-02 6.10e+03 2.78e+01 ... (remaining 15589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 20691 2.75 - 5.51: 605 5.51 - 8.26: 234 8.26 - 11.01: 11 11.01 - 13.76: 3 Bond angle restraints: 21544 Sorted by residual: angle pdb=" N TRP A 645 " pdb=" CA TRP A 645 " pdb=" C TRP A 645 " ideal model delta sigma weight residual 111.07 100.55 10.52 1.07e+00 8.73e-01 9.66e+01 angle pdb=" N ASP A 639 " pdb=" CA ASP A 639 " pdb=" C ASP A 639 " ideal model delta sigma weight residual 111.33 122.89 -11.56 1.21e+00 6.83e-01 9.13e+01 angle pdb=" N VAL A 637 " pdb=" CA VAL A 637 " pdb=" C VAL A 637 " ideal model delta sigma weight residual 111.00 101.46 9.54 1.09e+00 8.42e-01 7.66e+01 angle pdb=" C GLY A 619 " pdb=" N PRO A 620 " pdb=" CA PRO A 620 " ideal model delta sigma weight residual 119.32 128.78 -9.46 1.14e+00 7.69e-01 6.89e+01 angle pdb=" N ALA A 257 " pdb=" CA ALA A 257 " pdb=" C ALA A 257 " ideal model delta sigma weight residual 111.36 102.36 9.00 1.09e+00 8.42e-01 6.81e+01 ... (remaining 21539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 8989 16.01 - 32.02: 71 32.02 - 48.02: 33 48.02 - 64.03: 16 64.03 - 80.04: 2 Dihedral angle restraints: 9111 sinusoidal: 1193 harmonic: 7918 Sorted by residual: dihedral pdb=" C TYR J 105 " pdb=" N TYR J 105 " pdb=" CA TYR J 105 " pdb=" CB TYR J 105 " ideal model delta harmonic sigma weight residual -122.60 -103.38 -19.22 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" CB CYS K 192 " pdb=" SG CYS K 192 " pdb=" SG CYS K 222 " pdb=" CB CYS K 222 " ideal model delta sinusoidal sigma weight residual 93.00 152.47 -59.47 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS C 192 " pdb=" SG CYS C 192 " pdb=" SG CYS C 222 " pdb=" CB CYS C 222 " ideal model delta sinusoidal sigma weight residual 93.00 152.19 -59.19 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 9108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2321 0.084 - 0.168: 305 0.168 - 0.253: 22 0.253 - 0.337: 4 0.337 - 0.421: 4 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CA THR A 643 " pdb=" N THR A 643 " pdb=" C THR A 643 " pdb=" CB THR A 643 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA LEU A 805 " pdb=" N LEU A 805 " pdb=" C LEU A 805 " pdb=" CB LEU A 805 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CG LEU A 806 " pdb=" CB LEU A 806 " pdb=" CD1 LEU A 806 " pdb=" CD2 LEU A 806 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 2653 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 762 " -0.017 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C VAL A 762 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL A 762 " -0.025 2.00e-02 2.50e+03 pdb=" N GLN A 763 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 638 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LEU A 638 " -0.057 2.00e-02 2.50e+03 pdb=" O LEU A 638 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 639 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 233 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C ALA A 233 " -0.056 2.00e-02 2.50e+03 pdb=" O ALA A 233 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 234 " 0.019 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4786 2.80 - 3.33: 12849 3.33 - 3.85: 23389 3.85 - 4.38: 22958 4.38 - 4.90: 41184 Nonbonded interactions: 105166 Sorted by model distance: nonbonded pdb=" O VAL A 600 " pdb=" N ALA A 602 " model vdw 2.278 3.120 nonbonded pdb=" CB GLU H 82 " pdb=" OE1 GLN H 85 " model vdw 2.404 3.440 nonbonded pdb=" O TYR F 147 " pdb=" C GLY F 148 " model vdw 2.492 3.270 nonbonded pdb=" O TYR H 147 " pdb=" C GLY H 148 " model vdw 2.501 3.270 nonbonded pdb=" O TYR D 147 " pdb=" C GLY D 148 " model vdw 2.506 3.270 ... (remaining 105161 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 'B' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 56 or (resid 57 through 62 and (name N or name \ CA or name C or name O or name CB )) or (resid 63 through 68 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or na \ me CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 thro \ ugh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 thro \ ugh 98 or (resid 99 through 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 through 115 or (resid 116 and \ (name N or name CA or name C or name O or name CB )) or resid 117 through 146 or \ (resid 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 through 161 or (resid 162 through 165 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'D' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 65 or (resid 66 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 throu \ gh 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 99 or (resid 100 through 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 or (resid 112 through 113 and \ (name N or name CA or name C or name O or name CB )) or resid 114 through 115 or \ (resid 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 123 or (resid 124 through 131 and (name N or name CA or name C or name \ O or name CB )) or (resid 132 through 139 and (name N or name CA or name C or n \ ame O or name CB )) or resid 140 through 146 or (resid 147 and (name N or name C \ A or name C or name O or name CB )) or resid 148 or (resid 149 through 150 and ( \ name N or name CA or name C or name O or name CB )) or resid 151 through 161 or \ (resid 162 through 165 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'F' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 57 or (resid 58 through 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 83 or (resid 84 throug \ h 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 91 or (resid 92 through 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 115 or (resid 116 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 136 or (resid 137 through 139 and (nam \ e N or name CA or name C or name O or name CB )) or resid 140 through 146 or (re \ sid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 th \ rough 161 or (resid 162 through 165 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'H' and (resid 45 through 65 or (resid 66 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 throug \ h 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throug \ h 99 or (resid 100 through 102 and (name N or name CA or name C or name O or nam \ e CB )) or resid 103 through 104 or (resid 105 through 110 and (name N or name C \ A or name C or name O or name CB )) or resid 111 through 136 or (resid 137 throu \ gh 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thr \ ough 148 or (resid 149 through 150 and (name N or name CA or name C or name O or \ name CB )) or resid 151 through 161 or (resid 162 through 165 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 45 through 51 and (name N or name CA or name C or name O \ or name CB )) or resid 52 through 64 or (resid 65 through 68 and (name N or name \ CA or name C or name O or name CB )) or (resid 69 through 77 and (name N or nam \ e CA or name C or name O or name CB )) or resid 78 through 104 or (resid 105 thr \ ough 110 and (name N or name CA or name C or name O or name CB )) or resid 111 t \ hrough 146 or (resid 147 and (name N or name CA or name C or name O or name CB ) \ ) or resid 148 through 165)) } ncs_group { reference = (chain 'C' and (resid 30 through 41 or (resid 42 through 48 and (name N or name \ CA or name C or name O or name CB )) or (resid 49 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 63 or (resid 64 throug \ h 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throug \ h 117 or (resid 118 through 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 190 or (resid 191 and (name N or name CA or name C \ or name O or name CB )) or resid 192 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 504)) selection = (chain 'I' and (resid 30 through 165 or (resid 166 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 504)) } ncs_group { reference = (chain 'E' and (resid 30 through 163 or (resid 164 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 248)) selection = (chain 'G' and (resid 30 through 163 or (resid 164 through 168 and (name N or na \ me CA or name C or name O or name CB )) or resid 169 through 248)) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 16.580 Find NCS groups from input model: 0.290 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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 0.114 15609 Z= 0.498 Angle : 1.342 13.764 21574 Z= 0.946 Chirality : 0.057 0.421 2656 Planarity : 0.005 0.037 3056 Dihedral : 6.792 80.040 3954 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.59 % Favored : 97.16 % Rotamer: Outliers : 0.45 % Allowed : 0.89 % Favored : 98.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.16), residues: 2742 helix: 1.64 (0.16), residues: 771 sheet: 1.37 (0.21), residues: 661 loop : 0.09 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 753 TYR 0.037 0.004 TYR A 640 PHE 0.013 0.003 PHE F 97 TRP 0.015 0.004 TRP C 64 HIS 0.003 0.001 HIS A 622 Details of bonding type rmsd covalent geometry : bond 0.00754 (15594) covalent geometry : angle 1.33926 (21544) SS BOND : bond 0.03561 ( 15) SS BOND : angle 2.50375 ( 30) hydrogen bonds : bond 0.18848 ( 1082) hydrogen bonds : angle 6.99278 ( 3021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7865 (mt0) cc_final: 0.7579 (tm-30) REVERT: A 753 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8396 (mmm-85) REVERT: A 756 GLU cc_start: 0.8829 (tt0) cc_final: 0.7871 (tm-30) REVERT: D 66 LEU cc_start: 0.8618 (mp) cc_final: 0.8396 (mt) REVERT: J 105 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7223 (m-10) outliers start: 2 outliers final: 0 residues processed: 164 average time/residue: 0.1067 time to fit residues: 27.2875 Evaluate side-chains 108 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.178359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.146253 restraints weight = 39856.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.137343 restraints weight = 63010.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134063 restraints weight = 45190.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133397 restraints weight = 39925.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133812 restraints weight = 29628.958| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15609 Z= 0.221 Angle : 0.622 7.291 21574 Z= 0.351 Chirality : 0.044 0.197 2656 Planarity : 0.005 0.049 3056 Dihedral : 4.316 24.527 2839 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.45 % Allowed : 2.90 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.17), residues: 2742 helix: 2.88 (0.16), residues: 802 sheet: 0.99 (0.20), residues: 746 loop : 0.15 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 124 TYR 0.025 0.002 TYR H 114 PHE 0.022 0.002 PHE J 97 TRP 0.025 0.003 TRP H 117 HIS 0.011 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00424 (15594) covalent geometry : angle 0.61922 (21544) SS BOND : bond 0.00572 ( 15) SS BOND : angle 1.63496 ( 30) hydrogen bonds : bond 0.06140 ( 1082) hydrogen bonds : angle 4.75268 ( 3021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 222 MET cc_start: 0.8339 (mtp) cc_final: 0.7985 (mtp) REVERT: A 756 GLU cc_start: 0.8879 (tt0) cc_final: 0.7989 (tm-30) REVERT: I 161 TRP cc_start: 0.8556 (t60) cc_final: 0.8306 (t60) outliers start: 2 outliers final: 1 residues processed: 110 average time/residue: 0.0821 time to fit residues: 15.6655 Evaluate side-chains 90 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 34 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 chunk 209 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 176 optimal weight: 0.0040 chunk 222 optimal weight: 30.0000 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 50.0000 chunk 154 optimal weight: 10.0000 overall best weight: 1.0072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.177245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.147907 restraints weight = 40150.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.139409 restraints weight = 55713.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135096 restraints weight = 51168.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135497 restraints weight = 48943.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135212 restraints weight = 33192.395| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15609 Z= 0.160 Angle : 0.512 5.781 21574 Z= 0.291 Chirality : 0.043 0.179 2656 Planarity : 0.004 0.047 3056 Dihedral : 3.843 23.713 2839 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.17), residues: 2742 helix: 3.26 (0.16), residues: 801 sheet: 0.77 (0.19), residues: 749 loop : 0.25 (0.20), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 790 TYR 0.015 0.002 TYR B 114 PHE 0.028 0.002 PHE B 97 TRP 0.017 0.002 TRP B 117 HIS 0.007 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00319 (15594) covalent geometry : angle 0.51028 (21544) SS BOND : bond 0.00359 ( 15) SS BOND : angle 1.15422 ( 30) hydrogen bonds : bond 0.05298 ( 1082) hydrogen bonds : angle 4.22862 ( 3021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 612 MET cc_start: 0.8533 (tpt) cc_final: 0.8251 (tpt) REVERT: H 87 MET cc_start: 0.7020 (mtp) cc_final: 0.6748 (mtm) REVERT: I 161 TRP cc_start: 0.8661 (t60) cc_final: 0.8311 (t60) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0879 time to fit residues: 15.5415 Evaluate side-chains 80 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 63 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 80 optimal weight: 50.0000 chunk 246 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 242 optimal weight: 40.0000 chunk 37 optimal weight: 30.0000 chunk 0 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 222 optimal weight: 30.0000 chunk 202 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 HIS H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.171383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.142365 restraints weight = 39638.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.137512 restraints weight = 70613.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134572 restraints weight = 55957.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.134839 restraints weight = 59565.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134290 restraints weight = 45075.168| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 15609 Z= 0.305 Angle : 0.708 10.151 21574 Z= 0.405 Chirality : 0.047 0.212 2656 Planarity : 0.006 0.072 3056 Dihedral : 4.897 26.819 2839 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.89 % Allowed : 7.35 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.17), residues: 2742 helix: 2.70 (0.17), residues: 788 sheet: 0.11 (0.20), residues: 725 loop : -0.15 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 68 TYR 0.042 0.004 TYR D 105 PHE 0.048 0.005 PHE B 97 TRP 0.038 0.003 TRP B 117 HIS 0.014 0.004 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00639 (15594) covalent geometry : angle 0.70466 (21544) SS BOND : bond 0.00572 ( 15) SS BOND : angle 2.01635 ( 30) hydrogen bonds : bond 0.07191 ( 1082) hydrogen bonds : angle 4.96379 ( 3021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.8287 (ttt) cc_final: 0.7944 (ttt) REVERT: A 63 TRP cc_start: 0.8991 (t-100) cc_final: 0.8674 (t-100) REVERT: A 138 TYR cc_start: 0.8483 (p90) cc_final: 0.7992 (p90) REVERT: H 87 MET cc_start: 0.7418 (mtp) cc_final: 0.7146 (mtp) REVERT: H 100 MET cc_start: 0.6992 (mmp) cc_final: 0.6489 (mmm) REVERT: H 117 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.6333 (m100) REVERT: I 161 TRP cc_start: 0.9060 (t60) cc_final: 0.8748 (t60) outliers start: 4 outliers final: 2 residues processed: 89 average time/residue: 0.0761 time to fit residues: 12.3404 Evaluate side-chains 80 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 157 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 273 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 190 optimal weight: 0.2980 chunk 163 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.173376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.146628 restraints weight = 39993.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139839 restraints weight = 60651.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135479 restraints weight = 63167.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136301 restraints weight = 58435.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135617 restraints weight = 41181.262| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15609 Z= 0.220 Angle : 0.576 7.636 21574 Z= 0.324 Chirality : 0.044 0.195 2656 Planarity : 0.005 0.070 3056 Dihedral : 4.375 24.761 2839 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.17), residues: 2742 helix: 3.07 (0.17), residues: 787 sheet: 0.08 (0.20), residues: 697 loop : -0.22 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 608 TYR 0.025 0.003 TYR D 114 PHE 0.037 0.003 PHE D 95 TRP 0.057 0.002 TRP H 117 HIS 0.012 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00458 (15594) covalent geometry : angle 0.57433 (21544) SS BOND : bond 0.00557 ( 15) SS BOND : angle 1.22845 ( 30) hydrogen bonds : bond 0.05853 ( 1082) hydrogen bonds : angle 4.43395 ( 3021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 787 MET cc_start: 0.8134 (ttt) cc_final: 0.7794 (ttm) REVERT: H 100 MET cc_start: 0.6981 (mmp) cc_final: 0.6425 (mmm) REVERT: I 161 TRP cc_start: 0.9014 (t60) cc_final: 0.8707 (t60) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0816 time to fit residues: 12.6652 Evaluate side-chains 76 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 7 optimal weight: 0.7980 chunk 164 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 42 optimal weight: 40.0000 chunk 29 optimal weight: 0.0670 chunk 265 optimal weight: 30.0000 chunk 260 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 192 optimal weight: 10.0000 chunk 34 optimal weight: 40.0000 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.178430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.151337 restraints weight = 40209.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.144218 restraints weight = 61744.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140892 restraints weight = 58407.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141940 restraints weight = 51097.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.140931 restraints weight = 38152.146| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15609 Z= 0.109 Angle : 0.452 5.463 21574 Z= 0.250 Chirality : 0.042 0.140 2656 Planarity : 0.004 0.051 3056 Dihedral : 3.675 19.273 2839 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.17), residues: 2742 helix: 3.57 (0.16), residues: 790 sheet: 0.15 (0.19), residues: 732 loop : 0.01 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.012 0.001 TYR J 147 PHE 0.014 0.002 PHE H 144 TRP 0.018 0.001 TRP H 117 HIS 0.006 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00215 (15594) covalent geometry : angle 0.45206 (21544) SS BOND : bond 0.00190 ( 15) SS BOND : angle 0.68452 ( 30) hydrogen bonds : bond 0.04371 ( 1082) hydrogen bonds : angle 3.90801 ( 3021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: C 52 TYR cc_start: 0.8318 (t80) cc_final: 0.8078 (t80) REVERT: A 787 MET cc_start: 0.7806 (ttt) cc_final: 0.7422 (ttm) REVERT: H 87 MET cc_start: 0.6843 (mtp) cc_final: 0.6566 (mtm) REVERT: H 100 MET cc_start: 0.7803 (mmp) cc_final: 0.7183 (mmm) REVERT: I 161 TRP cc_start: 0.8960 (t60) cc_final: 0.8574 (t60) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0901 time to fit residues: 15.4987 Evaluate side-chains 84 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 23 optimal weight: 0.0000 chunk 67 optimal weight: 0.7980 chunk 130 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 chunk 195 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 134 optimal weight: 0.0970 chunk 189 optimal weight: 8.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.178659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149092 restraints weight = 39911.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139991 restraints weight = 64733.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138938 restraints weight = 53790.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137736 restraints weight = 45694.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.137927 restraints weight = 36013.535| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15609 Z= 0.098 Angle : 0.435 5.091 21574 Z= 0.238 Chirality : 0.041 0.136 2656 Planarity : 0.004 0.042 3056 Dihedral : 3.442 18.933 2839 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.17), residues: 2742 helix: 3.72 (0.16), residues: 792 sheet: 0.14 (0.19), residues: 746 loop : 0.22 (0.20), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.012 0.001 TYR A 640 PHE 0.015 0.001 PHE J 144 TRP 0.016 0.001 TRP H 117 HIS 0.004 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00193 (15594) covalent geometry : angle 0.43396 (21544) SS BOND : bond 0.00355 ( 15) SS BOND : angle 0.77855 ( 30) hydrogen bonds : bond 0.04022 ( 1082) hydrogen bonds : angle 3.67332 ( 3021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 645 TRP cc_start: 0.8067 (t-100) cc_final: 0.7461 (t-100) REVERT: A 787 MET cc_start: 0.7750 (ttt) cc_final: 0.7386 (ttm) REVERT: H 87 MET cc_start: 0.6906 (mtp) cc_final: 0.6572 (mtm) REVERT: H 100 MET cc_start: 0.7745 (mmp) cc_final: 0.7157 (mmm) REVERT: H 105 TYR cc_start: 0.8363 (p90) cc_final: 0.8124 (p90) REVERT: I 161 TRP cc_start: 0.8841 (t60) cc_final: 0.8632 (t60) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0770 time to fit residues: 13.5142 Evaluate side-chains 83 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 242 optimal weight: 40.0000 chunk 150 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 146 optimal weight: 40.0000 chunk 228 optimal weight: 50.0000 chunk 122 optimal weight: 0.9990 chunk 176 optimal weight: 0.0370 chunk 269 optimal weight: 0.3980 chunk 258 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.174210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.148585 restraints weight = 40097.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.141183 restraints weight = 58814.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.137071 restraints weight = 63108.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.138073 restraints weight = 58229.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137349 restraints weight = 39063.753| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15609 Z= 0.170 Angle : 0.509 5.804 21574 Z= 0.284 Chirality : 0.043 0.195 2656 Planarity : 0.004 0.057 3056 Dihedral : 3.793 26.151 2839 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.17), residues: 2742 helix: 3.77 (0.17), residues: 789 sheet: 0.14 (0.20), residues: 723 loop : 0.08 (0.20), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 89 TYR 0.020 0.002 TYR H 114 PHE 0.027 0.002 PHE D 95 TRP 0.031 0.002 TRP H 117 HIS 0.008 0.002 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00358 (15594) covalent geometry : angle 0.50848 (21544) SS BOND : bond 0.00226 ( 15) SS BOND : angle 0.91172 ( 30) hydrogen bonds : bond 0.04914 ( 1082) hydrogen bonds : angle 3.92516 ( 3021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.8954 (ttp) cc_final: 0.8642 (ttp) REVERT: H 100 MET cc_start: 0.6785 (mmp) cc_final: 0.6244 (mmm) REVERT: I 161 TRP cc_start: 0.8998 (t60) cc_final: 0.8760 (t60) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0796 time to fit residues: 12.8925 Evaluate side-chains 80 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 250 optimal weight: 0.8980 chunk 266 optimal weight: 0.5980 chunk 25 optimal weight: 0.0070 chunk 273 optimal weight: 0.0010 chunk 145 optimal weight: 0.7980 chunk 136 optimal weight: 0.0050 chunk 151 optimal weight: 40.0000 chunk 204 optimal weight: 20.0000 chunk 237 optimal weight: 50.0000 chunk 62 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 overall best weight: 0.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.175717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146982 restraints weight = 39974.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.139822 restraints weight = 62142.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136558 restraints weight = 55262.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136611 restraints weight = 48686.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136699 restraints weight = 34615.751| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15609 Z= 0.085 Angle : 0.419 4.850 21574 Z= 0.228 Chirality : 0.041 0.139 2656 Planarity : 0.004 0.041 3056 Dihedral : 3.283 18.311 2839 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.17), residues: 2742 helix: 3.84 (0.16), residues: 796 sheet: 0.28 (0.20), residues: 721 loop : 0.28 (0.20), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 198 TYR 0.011 0.001 TYR A 640 PHE 0.014 0.002 PHE J 144 TRP 0.011 0.001 TRP C 161 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00166 (15594) covalent geometry : angle 0.41894 (21544) SS BOND : bond 0.00217 ( 15) SS BOND : angle 0.69175 ( 30) hydrogen bonds : bond 0.03578 ( 1082) hydrogen bonds : angle 3.52030 ( 3021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.8813 (ttp) cc_final: 0.8510 (ttp) REVERT: H 100 MET cc_start: 0.7708 (mmp) cc_final: 0.7124 (mmm) REVERT: I 161 TRP cc_start: 0.8842 (t60) cc_final: 0.8620 (t60) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0794 time to fit residues: 14.0377 Evaluate side-chains 83 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 269 optimal weight: 0.5980 chunk 260 optimal weight: 0.0970 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 216 optimal weight: 0.4980 chunk 90 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 241 optimal weight: 30.0000 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.173279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.144731 restraints weight = 39683.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.137637 restraints weight = 58809.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132933 restraints weight = 56898.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134004 restraints weight = 50120.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132875 restraints weight = 33910.547| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15609 Z= 0.166 Angle : 0.492 5.831 21574 Z= 0.275 Chirality : 0.042 0.150 2656 Planarity : 0.004 0.055 3056 Dihedral : 3.634 22.763 2839 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.17), residues: 2742 helix: 3.86 (0.16), residues: 792 sheet: -0.03 (0.20), residues: 754 loop : 0.29 (0.20), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 89 TYR 0.016 0.002 TYR H 114 PHE 0.030 0.003 PHE D 95 TRP 0.030 0.002 TRP H 117 HIS 0.007 0.002 HIS D 72 Details of bonding type rmsd covalent geometry : bond 0.00353 (15594) covalent geometry : angle 0.49110 (21544) SS BOND : bond 0.00232 ( 15) SS BOND : angle 0.89730 ( 30) hydrogen bonds : bond 0.04653 ( 1082) hydrogen bonds : angle 3.78739 ( 3021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8906 (ttp) cc_final: 0.8607 (ttp) REVERT: H 100 MET cc_start: 0.7770 (mmp) cc_final: 0.7191 (mmm) REVERT: H 105 TYR cc_start: 0.8484 (p90) cc_final: 0.8276 (p90) REVERT: I 161 TRP cc_start: 0.9020 (t60) cc_final: 0.8778 (t60) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0770 time to fit residues: 12.4717 Evaluate side-chains 80 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 96 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 185 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.168847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141236 restraints weight = 39416.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.134058 restraints weight = 60443.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131013 restraints weight = 65098.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131142 restraints weight = 60754.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130485 restraints weight = 43634.422| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 15609 Z= 0.288 Angle : 0.661 9.827 21574 Z= 0.372 Chirality : 0.045 0.198 2656 Planarity : 0.005 0.071 3056 Dihedral : 4.600 34.930 2839 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.17), residues: 2742 helix: 3.20 (0.17), residues: 788 sheet: -0.16 (0.20), residues: 716 loop : -0.14 (0.19), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 89 TYR 0.039 0.003 TYR H 114 PHE 0.039 0.004 PHE B 97 TRP 0.039 0.003 TRP H 117 HIS 0.012 0.003 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00611 (15594) covalent geometry : angle 0.65703 (21544) SS BOND : bond 0.00686 ( 15) SS BOND : angle 2.05260 ( 30) hydrogen bonds : bond 0.06302 ( 1082) hydrogen bonds : angle 4.56772 ( 3021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2872.62 seconds wall clock time: 49 minutes 32.95 seconds (2972.95 seconds total)