Starting phenix.real_space_refine on Tue Jul 29 20:12:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8go8_34173/07_2025/8go8_34173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8go8_34173/07_2025/8go8_34173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8go8_34173/07_2025/8go8_34173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8go8_34173/07_2025/8go8_34173.map" model { file = "/net/cci-nas-00/data/ceres_data/8go8_34173/07_2025/8go8_34173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8go8_34173/07_2025/8go8_34173.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 74 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 38 5.16 5 C 7280 2.51 5 N 1938 2.21 5 O 2239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11505 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2803 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "V" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2808 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "U" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1363 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 7.00, per 1000 atoms: 0.61 Number of scatterers: 11505 At special positions: 0 Unit cell: (112.238, 201.413, 99.9375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 10 15.00 O 2239 8.00 N 1938 7.00 C 7280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.5 seconds 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 32 sheets defined 5.3% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.849A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.850A pdb=" N ARG B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.059A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 removed outlier: 4.241A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.060A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 129 removed outlier: 4.241A pdb=" N LYS M 127 " --> pdb=" O ASP M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 removed outlier: 3.830A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 85 removed outlier: 6.511A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 3.560A pdb=" N PHE A 349 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 316 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 117 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 75 removed outlier: 3.830A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 78 through 85 removed outlier: 6.510A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 183 through 189 Processing sheet with id=AB3, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.560A pdb=" N PHE B 349 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 316 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.868A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 15 removed outlier: 8.804A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.770A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AC1, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.868A pdb=" N VAL I 8 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 15 removed outlier: 8.803A pdb=" N SER I 35 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER I 55 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 14 through 15 removed outlier: 3.771A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY I 149 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR I 186 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY I 149 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR I 186 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 161 through 164 Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC8, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.529A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.529A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.636A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER L 177 " --> pdb=" O SER L 163 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AD3, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.528A pdb=" N GLU M 106 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.528A pdb=" N GLU M 106 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.635A pdb=" N SER M 115 " --> pdb=" O ASN M 138 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER M 177 " --> pdb=" O SER M 163 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1254 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: 3.70 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3708 1.34 - 1.46: 2688 1.46 - 1.58: 5291 1.58 - 1.69: 34 1.69 - 1.81: 48 Bond restraints: 11769 Sorted by residual: bond pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 ... (remaining 11764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 15894 2.48 - 4.96: 131 4.96 - 7.44: 18 7.44 - 9.92: 6 9.92 - 12.40: 8 Bond angle restraints: 16057 Sorted by residual: angle pdb=" CB TPO V 339 " pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 119.31 106.91 12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB TPO U 339 " pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 119.31 106.94 12.37 3.00e+00 1.11e-01 1.70e+01 angle pdb=" CB TPO U 342 " pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CB TPO V 336 " pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CB TPO U 336 " pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 119.31 107.12 12.19 3.00e+00 1.11e-01 1.65e+01 ... (remaining 16052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 6481 16.85 - 33.70: 458 33.70 - 50.54: 104 50.54 - 67.39: 14 67.39 - 84.24: 12 Dihedral angle restraints: 7069 sinusoidal: 2631 harmonic: 4438 Sorted by residual: dihedral pdb=" CB LYS A 226 " pdb=" CG LYS A 226 " pdb=" CD LYS A 226 " pdb=" CE LYS A 226 " ideal model delta sinusoidal sigma weight residual 60.00 116.52 -56.52 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CB LYS B 226 " pdb=" CG LYS B 226 " pdb=" CD LYS B 226 " pdb=" CE LYS B 226 " ideal model delta sinusoidal sigma weight residual 60.00 116.45 -56.45 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG ARG B 65 " pdb=" CD ARG B 65 " pdb=" NE ARG B 65 " pdb=" CZ ARG B 65 " ideal model delta sinusoidal sigma weight residual 180.00 139.48 40.52 2 1.50e+01 4.44e-03 9.00e+00 ... (remaining 7066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1026 0.026 - 0.052: 516 0.052 - 0.079: 102 0.079 - 0.105: 119 0.105 - 0.131: 73 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CA VAL L 95 " pdb=" N VAL L 95 " pdb=" C VAL L 95 " pdb=" CB VAL L 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA PHE U 335 " pdb=" N PHE U 335 " pdb=" C PHE U 335 " pdb=" CB PHE U 335 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 233 " pdb=" N ILE B 233 " pdb=" C ILE B 233 " pdb=" CB ILE B 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1833 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO H 159 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 358 " 0.006 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C GLU B 358 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU B 358 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 359 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 158 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO I 159 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 159 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 159 " -0.017 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2149 2.78 - 3.31: 9782 3.31 - 3.84: 17768 3.84 - 4.37: 20063 4.37 - 4.90: 37084 Nonbonded interactions: 86846 Sorted by model distance: nonbonded pdb=" NE2 GLN L 125 " pdb=" O THR L 130 " model vdw 2.253 3.120 nonbonded pdb=" NE2 GLN M 125 " pdb=" O THR M 130 " model vdw 2.254 3.120 nonbonded pdb=" O ALA B 301 " pdb=" OH TYR B 321 " model vdw 2.278 3.040 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.278 3.040 nonbonded pdb=" O ALA B 263 " pdb=" OG SER B 266 " model vdw 2.290 3.040 ... (remaining 86841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 368)) selection = (chain 'B' and (resid 7 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 311 or (resid 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 358 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 368)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 190)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.090 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.004 0.109 11775 Z= 0.213 Angle : 0.607 12.405 16069 Z= 0.270 Chirality : 0.042 0.131 1836 Planarity : 0.003 0.034 2058 Dihedral : 12.950 84.237 4191 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1478 helix: 0.56 (0.84), residues: 34 sheet: 1.29 (0.21), residues: 644 loop : 0.25 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.002 0.000 HIS B 353 PHE 0.008 0.001 PHE V 335 TYR 0.008 0.001 TYR M 50 ARG 0.005 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.24428 ( 424) hydrogen bonds : angle 9.52906 ( 1254) SS BOND : bond 0.00158 ( 6) SS BOND : angle 0.19994 ( 12) covalent geometry : bond 0.00433 (11769) covalent geometry : angle 0.60672 (16057) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8525 (ttmt) REVERT: A 294 LYS cc_start: 0.8092 (mttp) cc_final: 0.7793 (mtpp) REVERT: B 147 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8411 (ttmt) REVERT: B 294 LYS cc_start: 0.8154 (mttp) cc_final: 0.7880 (mtpp) REVERT: H 86 MET cc_start: 0.7239 (mtm) cc_final: 0.7013 (mtp) REVERT: H 210 HIS cc_start: 0.5789 (t-90) cc_final: 0.5149 (t-90) REVERT: I 210 HIS cc_start: 0.6173 (t-90) cc_final: 0.5274 (t-90) REVERT: L 161 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7373 (mm110) REVERT: M 5 MET cc_start: 0.8295 (mmm) cc_final: 0.8080 (mmt) REVERT: M 82 GLU cc_start: 0.7357 (pt0) cc_final: 0.7045 (pm20) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2906 time to fit residues: 78.6812 Evaluate side-chains 127 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.166023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113644 restraints weight = 16110.895| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.91 r_work: 0.3223 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11775 Z= 0.167 Angle : 0.588 14.418 16069 Z= 0.299 Chirality : 0.045 0.135 1836 Planarity : 0.004 0.040 2058 Dihedral : 4.333 39.546 1658 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.39 % Allowed : 7.38 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.23), residues: 1478 helix: 0.69 (0.70), residues: 50 sheet: 1.09 (0.20), residues: 708 loop : 0.31 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 164 HIS 0.004 0.001 HIS A 210 PHE 0.015 0.002 PHE M 117 TYR 0.024 0.002 TYR H 155 ARG 0.004 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 424) hydrogen bonds : angle 6.33652 ( 1254) SS BOND : bond 0.00461 ( 6) SS BOND : angle 0.65429 ( 12) covalent geometry : bond 0.00391 (11769) covalent geometry : angle 0.58819 (16057) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7316 (mt) cc_final: 0.7106 (mp) REVERT: A 161 ARG cc_start: 0.7455 (ptt-90) cc_final: 0.6739 (ptp90) REVERT: A 294 LYS cc_start: 0.8358 (mttp) cc_final: 0.8154 (mtpp) REVERT: A 352 MET cc_start: 0.8591 (mtm) cc_final: 0.8329 (mtm) REVERT: B 104 LEU cc_start: 0.7337 (mt) cc_final: 0.7129 (mp) REVERT: B 294 LYS cc_start: 0.8425 (mttp) cc_final: 0.8153 (mtpp) REVERT: B 295 HIS cc_start: 0.8629 (m-70) cc_final: 0.8384 (m-70) REVERT: B 352 MET cc_start: 0.8550 (mtm) cc_final: 0.8278 (mtm) REVERT: H 92 GLU cc_start: 0.8044 (pm20) cc_final: 0.7816 (pm20) REVERT: H 210 HIS cc_start: 0.5794 (t-170) cc_final: 0.5360 (t-90) REVERT: I 92 GLU cc_start: 0.8021 (pm20) cc_final: 0.7798 (pm20) REVERT: I 210 HIS cc_start: 0.5389 (t-170) cc_final: 0.4930 (t-90) REVERT: L 82 GLU cc_start: 0.7808 (pt0) cc_final: 0.7157 (pm20) REVERT: L 119 PHE cc_start: 0.5327 (m-80) cc_final: 0.5010 (m-80) REVERT: L 161 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7388 (mm110) REVERT: M 5 MET cc_start: 0.8801 (mmm) cc_final: 0.8425 (mmt) REVERT: M 82 GLU cc_start: 0.7790 (pt0) cc_final: 0.7160 (pm20) REVERT: M 119 PHE cc_start: 0.5454 (m-80) cc_final: 0.5159 (m-80) REVERT: M 161 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7510 (mm110) outliers start: 17 outliers final: 9 residues processed: 143 average time/residue: 0.2629 time to fit residues: 52.3505 Evaluate side-chains 130 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.165356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112670 restraints weight = 16341.759| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.96 r_work: 0.3209 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11775 Z= 0.156 Angle : 0.555 13.915 16069 Z= 0.280 Chirality : 0.044 0.144 1836 Planarity : 0.004 0.035 2058 Dihedral : 4.381 38.636 1658 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 9.35 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.22), residues: 1478 helix: 0.74 (0.78), residues: 48 sheet: 1.17 (0.20), residues: 698 loop : 0.13 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 164 HIS 0.003 0.001 HIS A 353 PHE 0.015 0.002 PHE M 117 TYR 0.026 0.002 TYR A 249 ARG 0.005 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 424) hydrogen bonds : angle 5.58356 ( 1254) SS BOND : bond 0.00382 ( 6) SS BOND : angle 0.62362 ( 12) covalent geometry : bond 0.00368 (11769) covalent geometry : angle 0.55526 (16057) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7474 (ptt-90) cc_final: 0.6599 (ptp90) REVERT: B 294 LYS cc_start: 0.8467 (mttp) cc_final: 0.8235 (mtpp) REVERT: B 352 MET cc_start: 0.8664 (mtm) cc_final: 0.8436 (mtm) REVERT: H 210 HIS cc_start: 0.5822 (t-170) cc_final: 0.5131 (t-90) REVERT: I 210 HIS cc_start: 0.5703 (t-170) cc_final: 0.5265 (t-90) REVERT: L 82 GLU cc_start: 0.7825 (pt0) cc_final: 0.7146 (pm20) REVERT: L 119 PHE cc_start: 0.5570 (m-80) cc_final: 0.5144 (m-80) REVERT: L 161 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7406 (mm110) REVERT: M 5 MET cc_start: 0.8615 (mmm) cc_final: 0.8322 (mmt) REVERT: M 82 GLU cc_start: 0.7931 (pt0) cc_final: 0.7180 (pm20) REVERT: M 119 PHE cc_start: 0.5482 (m-80) cc_final: 0.5047 (m-80) REVERT: M 161 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7624 (mm110) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.2709 time to fit residues: 47.4944 Evaluate side-chains 114 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 130 optimal weight: 0.9990 chunk 53 optimal weight: 0.0070 chunk 140 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN M 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.163686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114214 restraints weight = 15923.939| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.73 r_work: 0.3250 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11775 Z= 0.118 Angle : 0.515 14.115 16069 Z= 0.257 Chirality : 0.043 0.133 1836 Planarity : 0.003 0.034 2058 Dihedral : 4.330 40.482 1658 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.31 % Allowed : 9.60 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.22), residues: 1478 helix: 0.81 (0.76), residues: 48 sheet: 1.20 (0.20), residues: 698 loop : 0.12 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 164 HIS 0.002 0.000 HIS B 362 PHE 0.011 0.001 PHE B 277 TYR 0.010 0.001 TYR M 50 ARG 0.005 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 424) hydrogen bonds : angle 5.23147 ( 1254) SS BOND : bond 0.00338 ( 6) SS BOND : angle 0.43145 ( 12) covalent geometry : bond 0.00279 (11769) covalent geometry : angle 0.51471 (16057) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8241 (tptt) cc_final: 0.7991 (tptm) REVERT: A 161 ARG cc_start: 0.7439 (ptt-90) cc_final: 0.6567 (ptp90) REVERT: A 195 LYS cc_start: 0.8529 (mmmt) cc_final: 0.7640 (mtmt) REVERT: B 195 LYS cc_start: 0.8520 (mmmt) cc_final: 0.7634 (mtmt) REVERT: B 294 LYS cc_start: 0.8416 (mttp) cc_final: 0.8174 (mtpp) REVERT: H 92 GLU cc_start: 0.8029 (pm20) cc_final: 0.7815 (pm20) REVERT: H 210 HIS cc_start: 0.5779 (t-170) cc_final: 0.5355 (t-90) REVERT: L 82 GLU cc_start: 0.7837 (pt0) cc_final: 0.7120 (pm20) REVERT: L 119 PHE cc_start: 0.5635 (m-80) cc_final: 0.5110 (m-80) REVERT: L 161 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7443 (mm110) REVERT: L 184 LYS cc_start: 0.7196 (mmtt) cc_final: 0.6881 (mmtt) REVERT: M 5 MET cc_start: 0.8485 (mmm) cc_final: 0.8282 (mmt) REVERT: M 82 GLU cc_start: 0.7856 (pt0) cc_final: 0.7155 (pm20) REVERT: M 119 PHE cc_start: 0.5518 (m-80) cc_final: 0.4968 (m-80) REVERT: M 161 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7733 (mm110) REVERT: M 184 LYS cc_start: 0.7258 (mmtt) cc_final: 0.7057 (mmtt) outliers start: 16 outliers final: 4 residues processed: 123 average time/residue: 0.2530 time to fit residues: 43.8509 Evaluate side-chains 116 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 78 optimal weight: 0.0470 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.164483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112185 restraints weight = 16109.036| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.90 r_work: 0.3213 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11775 Z= 0.159 Angle : 0.538 13.955 16069 Z= 0.270 Chirality : 0.044 0.140 1836 Planarity : 0.003 0.034 2058 Dihedral : 4.404 39.959 1658 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.15 % Allowed : 10.99 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1478 helix: 0.79 (0.76), residues: 48 sheet: 1.17 (0.20), residues: 696 loop : 0.10 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 164 HIS 0.004 0.001 HIS I 210 PHE 0.015 0.001 PHE A 277 TYR 0.012 0.001 TYR L 92 ARG 0.005 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 424) hydrogen bonds : angle 5.17108 ( 1254) SS BOND : bond 0.00395 ( 6) SS BOND : angle 0.49864 ( 12) covalent geometry : bond 0.00379 (11769) covalent geometry : angle 0.53846 (16057) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.9045 (m-80) cc_final: 0.8682 (m-80) REVERT: A 161 ARG cc_start: 0.7445 (ptt-90) cc_final: 0.6574 (ptp90) REVERT: A 195 LYS cc_start: 0.8530 (mmmt) cc_final: 0.7694 (mtmt) REVERT: B 144 TYR cc_start: 0.9047 (m-80) cc_final: 0.8684 (m-80) REVERT: B 195 LYS cc_start: 0.8532 (mmmt) cc_final: 0.7689 (mtmt) REVERT: B 294 LYS cc_start: 0.8464 (mttp) cc_final: 0.8240 (mtpp) REVERT: H 92 GLU cc_start: 0.8065 (pm20) cc_final: 0.7830 (pm20) REVERT: H 210 HIS cc_start: 0.5864 (t-170) cc_final: 0.5316 (t-90) REVERT: L 82 GLU cc_start: 0.7906 (pt0) cc_final: 0.7148 (pm20) REVERT: L 117 PHE cc_start: 0.6602 (m-10) cc_final: 0.6396 (m-10) REVERT: L 119 PHE cc_start: 0.5448 (m-80) cc_final: 0.4825 (m-80) REVERT: L 161 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7305 (mm110) REVERT: L 184 LYS cc_start: 0.7170 (mmtt) cc_final: 0.6897 (mmtt) REVERT: M 5 MET cc_start: 0.8505 (mmm) cc_final: 0.8291 (mmt) REVERT: M 82 GLU cc_start: 0.7912 (pt0) cc_final: 0.7149 (pm20) REVERT: M 117 PHE cc_start: 0.6425 (m-10) cc_final: 0.6219 (m-10) REVERT: M 119 PHE cc_start: 0.5597 (m-80) cc_final: 0.4929 (m-80) outliers start: 14 outliers final: 5 residues processed: 128 average time/residue: 0.2524 time to fit residues: 45.7384 Evaluate side-chains 115 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 118 optimal weight: 0.0030 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.162491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112720 restraints weight = 16036.929| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.76 r_work: 0.3235 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11775 Z= 0.144 Angle : 0.535 13.791 16069 Z= 0.267 Chirality : 0.044 0.136 1836 Planarity : 0.003 0.032 2058 Dihedral : 4.422 41.414 1658 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.31 % Allowed : 11.89 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1478 helix: 0.89 (0.76), residues: 48 sheet: 1.21 (0.20), residues: 696 loop : 0.08 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 164 HIS 0.003 0.001 HIS B 362 PHE 0.012 0.001 PHE B 277 TYR 0.012 0.001 TYR L 92 ARG 0.006 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 424) hydrogen bonds : angle 5.04511 ( 1254) SS BOND : bond 0.00348 ( 6) SS BOND : angle 0.41979 ( 12) covalent geometry : bond 0.00344 (11769) covalent geometry : angle 0.53511 (16057) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.9007 (m-80) cc_final: 0.8682 (m-80) REVERT: A 161 ARG cc_start: 0.7431 (ptt-90) cc_final: 0.6575 (ptp90) REVERT: A 195 LYS cc_start: 0.8539 (mmmt) cc_final: 0.7698 (mtmt) REVERT: B 144 TYR cc_start: 0.9007 (m-80) cc_final: 0.8678 (m-80) REVERT: B 195 LYS cc_start: 0.8525 (mmmt) cc_final: 0.7682 (mtmt) REVERT: B 294 LYS cc_start: 0.8537 (mttp) cc_final: 0.8316 (mtpp) REVERT: H 155 TYR cc_start: 0.7771 (p90) cc_final: 0.7088 (p90) REVERT: H 210 HIS cc_start: 0.5929 (t-170) cc_final: 0.5550 (t-90) REVERT: L 82 GLU cc_start: 0.7888 (pt0) cc_final: 0.7162 (pm20) REVERT: L 161 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7329 (mm110) REVERT: M 5 MET cc_start: 0.8478 (mmm) cc_final: 0.8261 (mmt) REVERT: M 82 GLU cc_start: 0.7882 (pt0) cc_final: 0.7158 (pm20) REVERT: M 119 PHE cc_start: 0.5533 (m-80) cc_final: 0.4865 (m-80) outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 0.2655 time to fit residues: 47.9675 Evaluate side-chains 116 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.163295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110666 restraints weight = 16420.121| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.93 r_work: 0.3194 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11775 Z= 0.185 Angle : 0.562 13.810 16069 Z= 0.282 Chirality : 0.045 0.138 1836 Planarity : 0.004 0.031 2058 Dihedral : 4.507 41.843 1658 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.74 % Allowed : 13.54 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1478 helix: 1.00 (0.75), residues: 48 sheet: 1.09 (0.20), residues: 698 loop : 0.00 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 164 HIS 0.004 0.001 HIS B 362 PHE 0.012 0.002 PHE B 277 TYR 0.021 0.002 TYR I 155 ARG 0.007 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 424) hydrogen bonds : angle 5.08894 ( 1254) SS BOND : bond 0.00417 ( 6) SS BOND : angle 0.48665 ( 12) covalent geometry : bond 0.00447 (11769) covalent geometry : angle 0.56169 (16057) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.9072 (m-80) cc_final: 0.8803 (m-80) REVERT: A 161 ARG cc_start: 0.7412 (ptt-90) cc_final: 0.6558 (ptp90) REVERT: A 195 LYS cc_start: 0.8546 (mmmt) cc_final: 0.7754 (mtmt) REVERT: B 144 TYR cc_start: 0.9075 (m-80) cc_final: 0.8808 (m-80) REVERT: B 195 LYS cc_start: 0.8542 (mmmt) cc_final: 0.7717 (mtmt) REVERT: H 155 TYR cc_start: 0.7634 (p90) cc_final: 0.7029 (p90) REVERT: H 210 HIS cc_start: 0.5858 (t-170) cc_final: 0.5432 (t-90) REVERT: L 82 GLU cc_start: 0.7947 (pt0) cc_final: 0.7184 (pm20) REVERT: L 161 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7382 (mm110) REVERT: M 5 MET cc_start: 0.8582 (mmm) cc_final: 0.8267 (mmt) REVERT: M 82 GLU cc_start: 0.7938 (pt0) cc_final: 0.7175 (pm20) REVERT: M 117 PHE cc_start: 0.6438 (m-10) cc_final: 0.6228 (m-10) REVERT: M 119 PHE cc_start: 0.5617 (m-80) cc_final: 0.4954 (m-80) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.3418 time to fit residues: 55.3770 Evaluate side-chains 110 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain M residue 21 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.163968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111200 restraints weight = 16451.615| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.95 r_work: 0.3196 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11775 Z= 0.158 Angle : 0.541 13.768 16069 Z= 0.271 Chirality : 0.044 0.137 1836 Planarity : 0.003 0.031 2058 Dihedral : 4.483 43.495 1658 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.41 % Allowed : 14.60 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1478 helix: 1.17 (0.76), residues: 48 sheet: 1.07 (0.20), residues: 696 loop : -0.01 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 164 HIS 0.003 0.000 HIS B 362 PHE 0.012 0.001 PHE B 277 TYR 0.016 0.001 TYR I 155 ARG 0.006 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 424) hydrogen bonds : angle 4.97048 ( 1254) SS BOND : bond 0.00381 ( 6) SS BOND : angle 0.38167 ( 12) covalent geometry : bond 0.00381 (11769) covalent geometry : angle 0.54106 (16057) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.9057 (m-80) cc_final: 0.8779 (m-80) REVERT: A 161 ARG cc_start: 0.7335 (ptt-90) cc_final: 0.6575 (ptp90) REVERT: A 195 LYS cc_start: 0.8530 (mmmt) cc_final: 0.7738 (mtmt) REVERT: B 144 TYR cc_start: 0.9059 (m-80) cc_final: 0.8787 (m-80) REVERT: B 195 LYS cc_start: 0.8521 (mmmt) cc_final: 0.7706 (mtmt) REVERT: H 155 TYR cc_start: 0.7859 (p90) cc_final: 0.7356 (p90) REVERT: L 82 GLU cc_start: 0.7967 (pt0) cc_final: 0.7157 (pm20) REVERT: L 161 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7512 (mm110) REVERT: M 82 GLU cc_start: 0.7923 (pt0) cc_final: 0.7137 (pm20) REVERT: M 117 PHE cc_start: 0.6451 (m-10) cc_final: 0.6225 (m-10) REVERT: M 119 PHE cc_start: 0.5449 (m-80) cc_final: 0.4933 (m-80) outliers start: 5 outliers final: 5 residues processed: 112 average time/residue: 0.2748 time to fit residues: 42.7656 Evaluate side-chains 109 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain M residue 149 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 124 optimal weight: 0.0170 chunk 74 optimal weight: 0.2980 chunk 11 optimal weight: 0.0470 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 64 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 overall best weight: 0.1554 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.166769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114773 restraints weight = 16249.565| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.91 r_work: 0.3247 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11775 Z= 0.087 Angle : 0.506 14.314 16069 Z= 0.249 Chirality : 0.043 0.132 1836 Planarity : 0.003 0.033 2058 Dihedral : 4.302 46.359 1658 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.66 % Allowed : 14.36 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1478 helix: 1.28 (0.78), residues: 48 sheet: 1.27 (0.20), residues: 694 loop : 0.05 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 164 HIS 0.002 0.000 HIS B 353 PHE 0.014 0.001 PHE L 117 TYR 0.016 0.001 TYR I 155 ARG 0.009 0.000 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.02764 ( 424) hydrogen bonds : angle 4.58832 ( 1254) SS BOND : bond 0.00255 ( 6) SS BOND : angle 0.25406 ( 12) covalent geometry : bond 0.00202 (11769) covalent geometry : angle 0.50608 (16057) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8170 (m-80) cc_final: 0.7916 (m-80) REVERT: A 144 TYR cc_start: 0.9022 (m-80) cc_final: 0.8733 (m-80) REVERT: A 161 ARG cc_start: 0.7259 (ptt-90) cc_final: 0.6482 (ptp90) REVERT: A 195 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7665 (mtmt) REVERT: B 111 HIS cc_start: 0.7799 (m-70) cc_final: 0.7389 (m-70) REVERT: B 144 TYR cc_start: 0.9022 (m-80) cc_final: 0.8730 (m-80) REVERT: B 160 LYS cc_start: 0.8278 (tptt) cc_final: 0.8044 (tptm) REVERT: B 195 LYS cc_start: 0.8462 (mmmt) cc_final: 0.7625 (mtmt) REVERT: H 103 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8171 (ttp80) REVERT: H 155 TYR cc_start: 0.7766 (p90) cc_final: 0.7364 (p90) REVERT: I 103 ARG cc_start: 0.8437 (mtp-110) cc_final: 0.8177 (ttp80) REVERT: L 82 GLU cc_start: 0.7958 (pt0) cc_final: 0.7156 (pm20) REVERT: L 161 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7425 (mm110) REVERT: M 82 GLU cc_start: 0.7947 (pt0) cc_final: 0.7156 (pm20) outliers start: 8 outliers final: 3 residues processed: 124 average time/residue: 0.3591 time to fit residues: 64.1857 Evaluate side-chains 118 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain L residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 82 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 107 optimal weight: 8.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.162159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112638 restraints weight = 15914.401| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.72 r_work: 0.3231 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11775 Z= 0.147 Angle : 0.541 14.204 16069 Z= 0.267 Chirality : 0.043 0.138 1836 Planarity : 0.003 0.034 2058 Dihedral : 4.393 44.128 1658 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.41 % Allowed : 15.34 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1478 helix: 1.17 (0.77), residues: 48 sheet: 1.23 (0.20), residues: 696 loop : 0.09 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 164 HIS 0.003 0.001 HIS B 362 PHE 0.015 0.001 PHE M 119 TYR 0.011 0.001 TYR M 92 ARG 0.008 0.000 ARG B 312 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 424) hydrogen bonds : angle 4.66487 ( 1254) SS BOND : bond 0.00340 ( 6) SS BOND : angle 0.35575 ( 12) covalent geometry : bond 0.00356 (11769) covalent geometry : angle 0.54078 (16057) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.9018 (m-80) cc_final: 0.8735 (m-80) REVERT: A 161 ARG cc_start: 0.7199 (ptt-90) cc_final: 0.6540 (ptp90) REVERT: A 195 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7697 (mtmt) REVERT: B 144 TYR cc_start: 0.9021 (m-80) cc_final: 0.8742 (m-80) REVERT: B 195 LYS cc_start: 0.8497 (mmmt) cc_final: 0.7691 (mtmt) REVERT: B 359 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: H 155 TYR cc_start: 0.7930 (p90) cc_final: 0.7467 (p90) REVERT: L 82 GLU cc_start: 0.7946 (pt0) cc_final: 0.7156 (pm20) REVERT: M 82 GLU cc_start: 0.7943 (pt0) cc_final: 0.7154 (pm20) outliers start: 5 outliers final: 4 residues processed: 109 average time/residue: 0.2589 time to fit residues: 40.5397 Evaluate side-chains 108 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain L residue 149 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112384 restraints weight = 15989.705| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.73 r_work: 0.3228 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11775 Z= 0.141 Angle : 0.532 13.792 16069 Z= 0.266 Chirality : 0.044 0.138 1836 Planarity : 0.003 0.036 2058 Dihedral : 4.409 44.265 1658 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.49 % Allowed : 15.50 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1478 helix: 1.73 (0.78), residues: 48 sheet: 1.22 (0.20), residues: 696 loop : 0.05 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 164 HIS 0.002 0.000 HIS B 362 PHE 0.016 0.001 PHE M 119 TYR 0.011 0.001 TYR L 92 ARG 0.008 0.000 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.02981 ( 424) hydrogen bonds : angle 4.71898 ( 1254) SS BOND : bond 0.00332 ( 6) SS BOND : angle 0.39786 ( 12) covalent geometry : bond 0.00341 (11769) covalent geometry : angle 0.53208 (16057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6419.49 seconds wall clock time: 114 minutes 57.95 seconds (6897.95 seconds total)