Starting phenix.real_space_refine on Mon Jul 28 14:38:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci8_45614/07_2025/9ci8_45614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci8_45614/07_2025/9ci8_45614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ci8_45614/07_2025/9ci8_45614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci8_45614/07_2025/9ci8_45614.map" model { file = "/net/cci-nas-00/data/ceres_data/9ci8_45614/07_2025/9ci8_45614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci8_45614/07_2025/9ci8_45614.cif" } resolution = 3.01 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6698 2.51 5 N 1693 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 10466 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1496 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 196} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1491 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 183} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1513 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1557 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "b" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 248 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 643 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "e" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "f" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 972 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 795 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "m" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 8.05, per 1000 atoms: 0.77 Number of scatterers: 10466 At special positions: 0 Unit cell: (77.9, 173.02, 164.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2009 8.00 N 1693 7.00 C 6698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 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 1.2 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2582 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 27 sheets defined 22.1% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.671A pdb=" N ILE A 84 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.811A pdb=" N HIS C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.828A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 55 removed outlier: 3.727A pdb=" N PHE a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 56 Processing helix chain 'd' and resid 100 through 126 Processing helix chain 'e' and resid 88 through 93 removed outlier: 3.877A pdb=" N SER e 93 " --> pdb=" O GLU e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 3.901A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 93 removed outlier: 3.828A pdb=" N SER f 93 " --> pdb=" O GLU f 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 155 removed outlier: 3.657A pdb=" N SER f 152 " --> pdb=" O VAL f 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 25 through 29 removed outlier: 3.733A pdb=" N ASN g 28 " --> pdb=" O ILE g 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS g 29 " --> pdb=" O LYS g 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 25 through 29' Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 111 through 135 Processing helix chain 'm' and resid 239 through 271 Processing helix chain 'n' and resid 242 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.578A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120 removed outlier: 4.010A pdb=" N ASN A 139 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER A 133 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU A 183 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL A 135 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 181 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE A 137 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER A 179 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN A 139 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET A 177 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 176 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 157 removed outlier: 4.395A pdb=" N TRP A 150 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 196 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 209 " --> pdb=" O CYS A 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 207 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.503A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 34 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.830A pdb=" N TYR B 184 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.830A pdb=" N TYR B 184 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.545A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 120 removed outlier: 5.759A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.560A pdb=" N LYS C 209 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.558A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.431A pdb=" N CYS D 96 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP D 112 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG D 98 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.394A pdb=" N TYR D 184 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.394A pdb=" N TYR D 184 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 160 through 163 removed outlier: 3.540A pdb=" N THR D 160 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 26 through 29 removed outlier: 5.824A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 42 through 46 removed outlier: 5.153A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG e 115 " --> pdb=" O HIS d 89 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AC5, first strand: chain 'e' and resid 37 through 40 Processing sheet with id=AC6, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AC7, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.819A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AC9, first strand: chain 'g' and resid 31 through 33 removed outlier: 7.309A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU g 74 " --> pdb=" O VAL g 42 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1515 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: 3.45 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3252 1.35 - 1.47: 2704 1.47 - 1.59: 4636 1.59 - 1.71: 0 1.71 - 1.83: 93 Bond restraints: 10685 Sorted by residual: bond pdb=" CB ASP B 106 " pdb=" CG ASP B 106 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.54e+00 bond pdb=" CB GLU f 86 " pdb=" CG GLU f 86 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.59e+00 bond pdb=" N ASP f 63 " pdb=" CA ASP f 63 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.25e+00 bond pdb=" CA ASN g 111 " pdb=" CB ASN g 111 " ideal model delta sigma weight residual 1.527 1.551 -0.024 1.44e-02 4.82e+03 2.84e+00 bond pdb=" CA SER A 205 " pdb=" C SER A 205 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.47e+00 ... (remaining 10680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 14365 2.95 - 5.90: 139 5.90 - 8.84: 27 8.84 - 11.79: 3 11.79 - 14.74: 1 Bond angle restraints: 14535 Sorted by residual: angle pdb=" CB MET d 92 " pdb=" CG MET d 92 " pdb=" SD MET d 92 " ideal model delta sigma weight residual 112.70 127.44 -14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CB ILE f 66 " pdb=" CG1 ILE f 66 " pdb=" CD1 ILE f 66 " ideal model delta sigma weight residual 113.80 122.35 -8.55 2.10e+00 2.27e-01 1.66e+01 angle pdb=" CA GLU f 86 " pdb=" CB GLU f 86 " pdb=" CG GLU f 86 " ideal model delta sigma weight residual 114.10 122.24 -8.14 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA ILE f 66 " pdb=" CB ILE f 66 " pdb=" CG1 ILE f 66 " ideal model delta sigma weight residual 110.40 117.13 -6.73 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CB GLU f 86 " pdb=" CG GLU f 86 " pdb=" CD GLU f 86 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.70e+00 3.46e-01 1.54e+01 ... (remaining 14530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5399 17.13 - 34.26: 680 34.26 - 51.39: 210 51.39 - 68.52: 37 68.52 - 85.65: 11 Dihedral angle restraints: 6337 sinusoidal: 2322 harmonic: 4015 Sorted by residual: dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -35.66 -50.34 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CA ILE D 51 " pdb=" C ILE D 51 " pdb=" N ASN D 52 " pdb=" CA ASN D 52 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CB CYS f 119 " pdb=" SG CYS f 119 " pdb=" SG CYS f 122 " pdb=" CB CYS f 122 " ideal model delta sinusoidal sigma weight residual -86.00 -127.07 41.07 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 6334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1336 0.056 - 0.111: 308 0.111 - 0.167: 52 0.167 - 0.222: 5 0.222 - 0.278: 3 Chirality restraints: 1704 Sorted by residual: chirality pdb=" CB VAL e 118 " pdb=" CA VAL e 118 " pdb=" CG1 VAL e 118 " pdb=" CG2 VAL e 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CG LEU m 250 " pdb=" CB LEU m 250 " pdb=" CD1 LEU m 250 " pdb=" CD2 LEU m 250 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ASN A 78 " pdb=" N ASN A 78 " pdb=" C ASN A 78 " pdb=" CB ASN A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1701 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR n 253 " 0.016 2.00e-02 2.50e+03 2.18e-02 9.53e+00 pdb=" CG TYR n 253 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR n 253 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR n 253 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR n 253 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR n 253 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR n 253 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR n 253 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 52 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C THR C 52 " -0.050 2.00e-02 2.50e+03 pdb=" O THR C 52 " 0.018 2.00e-02 2.50e+03 pdb=" N SER C 53 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 155 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.14e+00 pdb=" N PRO D 156 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " -0.025 5.00e-02 4.00e+02 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2262 2.79 - 3.32: 8951 3.32 - 3.84: 18334 3.84 - 4.37: 19851 4.37 - 4.90: 35278 Nonbonded interactions: 84676 Sorted by model distance: nonbonded pdb=" OH TYR C 37 " pdb=" OE1 GLN C 90 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP A 83 " pdb=" OH TYR A 87 " model vdw 2.260 3.040 nonbonded pdb=" O SER e 41 " pdb=" OG SER e 41 " model vdw 2.295 3.040 nonbonded pdb=" O ASP f 137 " pdb=" OG1 THR f 141 " model vdw 2.304 3.040 nonbonded pdb=" O GLN f 92 " pdb=" OH TYR f 96 " model vdw 2.326 3.040 ... (remaining 84671 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 2 through 143 or (resid 144 and (name N or name CA or name \ C or name O or name CB )) or resid 145 through 148 or (resid 149 through 150 an \ d (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or resid 161 through 171 or (resid 172 and (name N or name CA or name C or name \ O or name CB )) or resid 173 through 200 or resid 207 through 213)) selection = (chain 'C' and (resid 2 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 24 or (resid 25 through 29 \ and (name N or name CA or name C or name O or name CB )) or resid 30 through 53 \ or (resid 54 through 55 and (name N or name CA or name C or name O or name CB )) \ or resid 56 through 58 or (resid 59 and (name N or name CA or name C or name O \ or name CB )) or resid 60 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 105 or resid 111 through 161 or ( \ resid 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ through 168 or (resid 169 through 172 and (name N or name CA or name C or name O \ or name CB )) or resid 173 through 181 or (resid 182 and (name N or name CA or \ name C or name O or name CB )) or resid 183 or (resid 184 through 190 and (name \ N or name CA or name C or name O or name CB )) or resid 191 through 213)) } ncs_group { reference = (chain 'B' and (resid 1 through 109 or (resid 110 and (name N or name CA or name \ C or name O or name CB )) or resid 111 through 123 or (resid 124 and (name N or \ name CA or name C or name O or name CB )) or resid 125 through 215 or (resid 21 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 217 through \ 221 or (resid 222 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 19 or (resid 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 82 or (resid 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 115 or (re \ sid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 th \ rough 120 or (resid 121 and (name N or name CA or name C or name O or name CB )) \ or resid 123 through 135 or resid 144 through 165 or resid 172 through 190 or r \ esid 202 through 222)) } ncs_group { reference = chain 'a' selection = (chain 'b' and resid 29 through 55) } ncs_group { reference = (chain 'e' and (resid 33 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 154)) selection = (chain 'f' and (resid 33 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 through 154)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 50.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.700 Find NCS groups from input model: 0.380 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 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 0.057 10702 Z= 0.179 Angle : 0.802 14.739 14569 Z= 0.421 Chirality : 0.049 0.278 1704 Planarity : 0.005 0.051 1804 Dihedral : 16.954 85.653 3704 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.93 % Allowed : 27.38 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: -0.84 (0.21), residues: 1330 helix: -0.49 (0.28), residues: 266 sheet: -0.03 (0.24), residues: 455 loop : -0.89 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 97 HIS 0.007 0.001 HIS d 89 PHE 0.029 0.002 PHE A 141 TYR 0.053 0.002 TYR n 253 ARG 0.007 0.001 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.13718 ( 536) hydrogen bonds : angle 7.32627 ( 1515) SS BOND : bond 0.00228 ( 17) SS BOND : angle 0.78327 ( 34) covalent geometry : bond 0.00365 (10685) covalent geometry : angle 0.80250 (14535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6093 (m100) cc_final: 0.5751 (m-10) REVERT: d 44 VAL cc_start: 0.5438 (OUTLIER) cc_final: 0.5233 (t) REVERT: e 56 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6543 (tp30) REVERT: e 121 ASN cc_start: 0.6676 (t0) cc_final: 0.6339 (t0) REVERT: e 145 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3136 (pp) REVERT: f 96 TYR cc_start: 0.8023 (m-80) cc_final: 0.7591 (m-80) REVERT: f 111 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.5934 (t80) REVERT: f 149 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.4242 (t80) REVERT: g 84 MET cc_start: 0.3717 (mmm) cc_final: 0.2926 (ttm) REVERT: n 253 TYR cc_start: 0.7683 (m-80) cc_final: 0.7357 (m-80) outliers start: 56 outliers final: 24 residues processed: 263 average time/residue: 0.2030 time to fit residues: 76.8562 Evaluate side-chains 198 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN C 212 ASN f 61 HIS f 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.210890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.178355 restraints weight = 13142.321| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 2.72 r_work: 0.4053 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 : 0.005 0.040 10702 Z= 0.200 Angle : 0.639 7.636 14569 Z= 0.335 Chirality : 0.044 0.209 1704 Planarity : 0.005 0.049 1804 Dihedral : 7.057 59.943 1509 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 7.48 % Allowed : 24.47 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: -0.40 (0.22), residues: 1330 helix: 0.74 (0.30), residues: 272 sheet: -0.12 (0.24), residues: 469 loop : -0.76 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 36 HIS 0.004 0.001 HIS f 61 PHE 0.019 0.002 PHE A 99 TYR 0.020 0.002 TYR C 87 ARG 0.003 0.001 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 536) hydrogen bonds : angle 5.83965 ( 1515) SS BOND : bond 0.00734 ( 17) SS BOND : angle 0.80073 ( 34) covalent geometry : bond 0.00453 (10685) covalent geometry : angle 0.63892 (14535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 167 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6297 (mt-10) cc_final: 0.5930 (tt0) REVERT: B 66 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6949 (p0) REVERT: C 24 CYS cc_start: 0.5225 (t) cc_final: 0.4979 (t) REVERT: C 152 ILE cc_start: 0.4898 (OUTLIER) cc_final: 0.4499 (tt) REVERT: D 163 TRP cc_start: 0.6333 (m100) cc_final: 0.5938 (m-10) REVERT: D 180 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.5724 (mttt) REVERT: d 44 VAL cc_start: 0.5378 (OUTLIER) cc_final: 0.5090 (t) REVERT: e 56 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6704 (tp30) REVERT: e 121 ASN cc_start: 0.7165 (t0) cc_final: 0.6833 (t0) REVERT: f 111 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6416 (t80) REVERT: f 149 TYR cc_start: 0.5489 (OUTLIER) cc_final: 0.4815 (t80) outliers start: 85 outliers final: 48 residues processed: 236 average time/residue: 0.1688 time to fit residues: 60.7195 Evaluate side-chains 215 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 41 SER Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 243 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 200 HIS C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.212919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167591 restraints weight = 13145.047| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.53 r_work: 0.4047 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10702 Z= 0.186 Angle : 0.621 7.137 14569 Z= 0.322 Chirality : 0.044 0.208 1704 Planarity : 0.004 0.046 1804 Dihedral : 6.188 58.833 1482 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.43 % Allowed : 26.32 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1330 helix: 1.34 (0.30), residues: 272 sheet: -0.16 (0.24), residues: 469 loop : -0.75 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 47 HIS 0.003 0.001 HIS C 191 PHE 0.017 0.002 PHE A 99 TYR 0.022 0.002 TYR A 72 ARG 0.003 0.000 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 536) hydrogen bonds : angle 5.56267 ( 1515) SS BOND : bond 0.00333 ( 17) SS BOND : angle 0.76626 ( 34) covalent geometry : bond 0.00424 (10685) covalent geometry : angle 0.62022 (14535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 168 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5363 (tt0) REVERT: B 154 TYR cc_start: 0.5737 (p90) cc_final: 0.5520 (p90) REVERT: D 163 TRP cc_start: 0.6715 (m100) cc_final: 0.6124 (m-10) REVERT: d 44 VAL cc_start: 0.5611 (OUTLIER) cc_final: 0.5231 (t) REVERT: e 56 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: f 111 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6603 (t80) REVERT: f 149 TYR cc_start: 0.5997 (OUTLIER) cc_final: 0.5181 (t80) outliers start: 73 outliers final: 51 residues processed: 225 average time/residue: 0.1816 time to fit residues: 61.9400 Evaluate side-chains 213 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 250 SER Chi-restraints excluded: chain n residue 269 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.206083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.162306 restraints weight = 13083.306| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.34 r_work: 0.4010 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10702 Z= 0.196 Angle : 0.626 7.130 14569 Z= 0.325 Chirality : 0.044 0.223 1704 Planarity : 0.004 0.049 1804 Dihedral : 6.049 59.857 1478 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 7.57 % Allowed : 26.67 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1330 helix: 1.61 (0.30), residues: 272 sheet: -0.27 (0.23), residues: 476 loop : -0.76 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 47 HIS 0.003 0.001 HIS C 191 PHE 0.019 0.002 PHE m 264 TYR 0.018 0.002 TYR C 87 ARG 0.003 0.000 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 536) hydrogen bonds : angle 5.52397 ( 1515) SS BOND : bond 0.00478 ( 17) SS BOND : angle 0.80510 ( 34) covalent geometry : bond 0.00453 (10685) covalent geometry : angle 0.62547 (14535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 159 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.6529 (p0) cc_final: 0.6210 (p0) REVERT: A 80 GLU cc_start: 0.6032 (mt-10) cc_final: 0.5389 (tt0) REVERT: D 163 TRP cc_start: 0.6722 (m100) cc_final: 0.6497 (m100) REVERT: D 180 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6055 (mttm) REVERT: e 56 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: e 121 ASN cc_start: 0.7548 (t0) cc_final: 0.7187 (t0) REVERT: f 46 ILE cc_start: 0.8478 (mt) cc_final: 0.8214 (mt) REVERT: f 111 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6756 (t80) REVERT: f 149 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.5063 (t80) outliers start: 86 outliers final: 58 residues processed: 227 average time/residue: 0.1704 time to fit residues: 59.2301 Evaluate side-chains 216 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 123 optimal weight: 0.3980 chunk 26 optimal weight: 0.0010 chunk 100 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.208328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164855 restraints weight = 13140.646| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.33 r_work: 0.4047 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10702 Z= 0.141 Angle : 0.583 8.717 14569 Z= 0.300 Chirality : 0.042 0.202 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.766 59.936 1476 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.25 % Allowed : 27.02 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: -0.03 (0.22), residues: 1330 helix: 1.90 (0.30), residues: 272 sheet: -0.28 (0.23), residues: 478 loop : -0.64 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 47 HIS 0.002 0.001 HIS d 89 PHE 0.012 0.001 PHE A 141 TYR 0.013 0.001 TYR C 142 ARG 0.003 0.000 ARG m 253 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 536) hydrogen bonds : angle 5.28034 ( 1515) SS BOND : bond 0.00279 ( 17) SS BOND : angle 0.68812 ( 34) covalent geometry : bond 0.00324 (10685) covalent geometry : angle 0.58255 (14535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6689 (m100) cc_final: 0.6154 (m-10) REVERT: D 180 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6361 (mttm) REVERT: e 41 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7532 (m) REVERT: e 121 ASN cc_start: 0.7527 (t0) cc_final: 0.7221 (t0) REVERT: f 46 ILE cc_start: 0.8477 (mt) cc_final: 0.8194 (mt) REVERT: f 111 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.6647 (t80) REVERT: f 149 TYR cc_start: 0.5543 (OUTLIER) cc_final: 0.4943 (t80) outliers start: 71 outliers final: 52 residues processed: 225 average time/residue: 0.1830 time to fit residues: 62.7550 Evaluate side-chains 210 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 86 GLN Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 82 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.207746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.164039 restraints weight = 13259.209| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.37 r_work: 0.4032 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10702 Z= 0.152 Angle : 0.596 10.113 14569 Z= 0.306 Chirality : 0.043 0.222 1704 Planarity : 0.004 0.048 1804 Dihedral : 5.561 58.447 1473 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 7.22 % Allowed : 26.41 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: 0.02 (0.22), residues: 1330 helix: 2.02 (0.30), residues: 272 sheet: -0.27 (0.23), residues: 479 loop : -0.63 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 163 HIS 0.003 0.001 HIS C 191 PHE 0.013 0.001 PHE A 99 TYR 0.016 0.001 TYR B 108 ARG 0.002 0.000 ARG m 253 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 536) hydrogen bonds : angle 5.25557 ( 1515) SS BOND : bond 0.00313 ( 17) SS BOND : angle 0.71201 ( 34) covalent geometry : bond 0.00350 (10685) covalent geometry : angle 0.59602 (14535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6705 (m100) cc_final: 0.6474 (m100) REVERT: D 180 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6381 (mttt) REVERT: e 41 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7537 (m) REVERT: e 121 ASN cc_start: 0.7591 (t0) cc_final: 0.7285 (t0) REVERT: f 46 ILE cc_start: 0.8483 (mt) cc_final: 0.8200 (mt) REVERT: f 111 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6658 (t80) REVERT: f 149 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.4898 (t80) outliers start: 82 outliers final: 62 residues processed: 223 average time/residue: 0.1878 time to fit residues: 65.4619 Evaluate side-chains 219 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 153 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.208747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.165426 restraints weight = 13297.814| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.38 r_work: 0.4043 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10702 Z= 0.143 Angle : 0.606 10.777 14569 Z= 0.308 Chirality : 0.043 0.227 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.408 58.362 1471 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.25 % Allowed : 27.46 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: 0.04 (0.23), residues: 1330 helix: 2.09 (0.30), residues: 272 sheet: -0.28 (0.23), residues: 462 loop : -0.62 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 163 HIS 0.003 0.001 HIS C 191 PHE 0.013 0.001 PHE A 211 TYR 0.026 0.001 TYR g 85 ARG 0.002 0.000 ARG m 253 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 536) hydrogen bonds : angle 5.20320 ( 1515) SS BOND : bond 0.00278 ( 17) SS BOND : angle 0.72549 ( 34) covalent geometry : bond 0.00330 (10685) covalent geometry : angle 0.60585 (14535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 159 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: C 24 CYS cc_start: 0.5263 (t) cc_final: 0.4979 (t) REVERT: D 163 TRP cc_start: 0.6605 (m100) cc_final: 0.6069 (m-10) REVERT: D 180 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6414 (mttt) REVERT: e 121 ASN cc_start: 0.7598 (t0) cc_final: 0.7299 (t0) REVERT: f 46 ILE cc_start: 0.8428 (mt) cc_final: 0.8147 (mt) REVERT: f 111 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6672 (t80) REVERT: f 149 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.4781 (t80) outliers start: 71 outliers final: 58 residues processed: 218 average time/residue: 0.1774 time to fit residues: 59.5448 Evaluate side-chains 217 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 156 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.209369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166352 restraints weight = 13207.092| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 2.36 r_work: 0.4058 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10702 Z= 0.133 Angle : 0.603 11.208 14569 Z= 0.305 Chirality : 0.043 0.254 1704 Planarity : 0.004 0.047 1804 Dihedral : 5.333 57.895 1471 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 6.95 % Allowed : 27.02 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: 0.12 (0.23), residues: 1330 helix: 2.21 (0.30), residues: 272 sheet: -0.28 (0.23), residues: 471 loop : -0.55 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 163 HIS 0.002 0.001 HIS d 89 PHE 0.014 0.001 PHE m 264 TYR 0.012 0.001 TYR D 108 ARG 0.003 0.000 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.02844 ( 536) hydrogen bonds : angle 5.10570 ( 1515) SS BOND : bond 0.00249 ( 17) SS BOND : angle 0.77809 ( 34) covalent geometry : bond 0.00306 (10685) covalent geometry : angle 0.60301 (14535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 162 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 141 PHE cc_start: 0.6312 (p90) cc_final: 0.6021 (p90) REVERT: D 163 TRP cc_start: 0.6628 (m100) cc_final: 0.6197 (m-10) REVERT: D 180 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6352 (mttt) REVERT: d 98 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7546 (tt0) REVERT: e 121 ASN cc_start: 0.7569 (t0) cc_final: 0.7266 (t0) REVERT: f 46 ILE cc_start: 0.8436 (mt) cc_final: 0.8160 (mt) REVERT: f 111 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6645 (t80) REVERT: f 149 TYR cc_start: 0.5329 (OUTLIER) cc_final: 0.4813 (t80) outliers start: 79 outliers final: 62 residues processed: 227 average time/residue: 0.2294 time to fit residues: 78.5356 Evaluate side-chains 223 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 158 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 28 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.205288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.165166 restraints weight = 13417.452| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.36 r_work: 0.4007 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10702 Z= 0.209 Angle : 0.673 11.120 14569 Z= 0.343 Chirality : 0.045 0.282 1704 Planarity : 0.004 0.049 1804 Dihedral : 5.628 55.694 1471 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 6.60 % Allowed : 27.46 % Favored : 65.93 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: -0.10 (0.23), residues: 1330 helix: 2.08 (0.30), residues: 271 sheet: -0.44 (0.23), residues: 477 loop : -0.68 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 163 HIS 0.003 0.001 HIS C 191 PHE 0.019 0.002 PHE A 99 TYR 0.018 0.002 TYR D 108 ARG 0.003 0.000 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 536) hydrogen bonds : angle 5.39892 ( 1515) SS BOND : bond 0.00454 ( 17) SS BOND : angle 1.16029 ( 34) covalent geometry : bond 0.00487 (10685) covalent geometry : angle 0.67184 (14535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 158 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 180 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6414 (mttt) REVERT: d 98 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7576 (tt0) REVERT: f 46 ILE cc_start: 0.8472 (mt) cc_final: 0.8199 (mt) REVERT: f 111 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6910 (t80) REVERT: f 149 TYR cc_start: 0.5389 (OUTLIER) cc_final: 0.4768 (t80) REVERT: g 43 LEU cc_start: 0.3822 (mt) cc_final: 0.3592 (mt) outliers start: 75 outliers final: 65 residues processed: 218 average time/residue: 0.1732 time to fit residues: 57.5553 Evaluate side-chains 221 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 153 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.206126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164825 restraints weight = 13211.920| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.42 r_work: 0.4011 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10702 Z= 0.181 Angle : 0.664 11.661 14569 Z= 0.336 Chirality : 0.044 0.284 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.592 56.190 1471 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.07 % Allowed : 28.35 % Favored : 65.58 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: -0.07 (0.22), residues: 1330 helix: 2.11 (0.30), residues: 271 sheet: -0.44 (0.23), residues: 480 loop : -0.65 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 163 HIS 0.003 0.001 HIS d 89 PHE 0.020 0.002 PHE m 264 TYR 0.018 0.002 TYR C 142 ARG 0.003 0.000 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 536) hydrogen bonds : angle 5.35264 ( 1515) SS BOND : bond 0.00337 ( 17) SS BOND : angle 0.95780 ( 34) covalent geometry : bond 0.00423 (10685) covalent geometry : angle 0.66338 (14535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 156 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 180 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6395 (mttt) REVERT: d 98 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7567 (tt0) REVERT: f 46 ILE cc_start: 0.8472 (mt) cc_final: 0.8209 (mt) REVERT: f 111 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6865 (t80) REVERT: f 149 TYR cc_start: 0.5464 (OUTLIER) cc_final: 0.4798 (t80) outliers start: 69 outliers final: 64 residues processed: 215 average time/residue: 0.1737 time to fit residues: 56.9994 Evaluate side-chains 220 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 153 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 0.1980 chunk 113 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.206303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.166841 restraints weight = 13189.064| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 2.31 r_work: 0.4019 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10702 Z= 0.176 Angle : 0.655 11.984 14569 Z= 0.333 Chirality : 0.044 0.285 1704 Planarity : 0.004 0.047 1804 Dihedral : 5.575 56.243 1471 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.16 % Allowed : 28.43 % Favored : 65.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % 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: -0.07 (0.22), residues: 1330 helix: 2.11 (0.30), residues: 272 sheet: -0.46 (0.23), residues: 480 loop : -0.63 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 163 HIS 0.003 0.001 HIS d 89 PHE 0.015 0.002 PHE A 99 TYR 0.016 0.002 TYR C 142 ARG 0.003 0.000 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 536) hydrogen bonds : angle 5.34057 ( 1515) SS BOND : bond 0.00334 ( 17) SS BOND : angle 0.90695 ( 34) covalent geometry : bond 0.00409 (10685) covalent geometry : angle 0.65477 (14535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10000.02 seconds wall clock time: 175 minutes 53.11 seconds (10553.11 seconds total)