Starting phenix.real_space_refine on Wed Feb 4 11:20:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci8_45614/02_2026/9ci8_45614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci8_45614/02_2026/9ci8_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_45614/02_2026/9ci8_45614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci8_45614/02_2026/9ci8_45614.map" model { file = "/net/cci-nas-00/data/ceres_data/9ci8_45614/02_2026/9ci8_45614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci8_45614/02_2026/9ci8_45614.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 1} 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: {'GLU:plan': 1, 'PHE: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: {'ASP:plan': 2, 'ARG:plan': 1} 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, 'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2} 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, 'ASP:plan': 1, 'ARG: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: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} 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: 2.78, per 1000 atoms: 0.27 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: 0.84 Conformation dependent library (CDL) restraints added in 560.9 milliseconds 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: 0.36 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: 2.02 Time building geometry restraints manager: 1.16 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: 9.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.150 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- 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 : 6.29 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.007 0.001 ARG g 82 TYR 0.053 0.002 TYR n 253 PHE 0.029 0.002 PHE A 141 TRP 0.017 0.002 TRP C 97 HIS 0.007 0.001 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00365 (10685) covalent geometry : angle 0.80250 (14535) SS BOND : bond 0.00228 ( 17) SS BOND : angle 0.78327 ( 34) hydrogen bonds : bond 0.13718 ( 536) hydrogen bonds : angle 7.32627 ( 1515) *********************** 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 : 0.411 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: 0.5232 (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: 0.6338 (t0) REVERT: e 145 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3138 (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: 0.4244 (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: 0.7358 (m-80) outliers start: 56 outliers final: 24 residues processed: 263 average time/residue: 0.0922 time to fit residues: 35.4463 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 : 0.425 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0050 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.213811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.180662 restraints weight = 13176.400| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.92 r_work: 0.4094 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1609 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= 0.164 Angle : 0.605 6.956 14569 Z= 0.317 Chirality : 0.043 0.201 1704 Planarity : 0.004 0.048 1804 Dihedral : 6.920 57.686 1509 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.34 % Allowed : 24.74 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1330 helix: 0.87 (0.30), residues: 272 sheet: 0.00 (0.24), residues: 468 loop : -0.69 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 102 TYR 0.019 0.002 TYR A 72 PHE 0.014 0.002 PHE A 99 TRP 0.011 0.002 TRP B 112 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00372 (10685) covalent geometry : angle 0.60424 (14535) SS BOND : bond 0.00390 ( 17) SS BOND : angle 0.81080 ( 34) hydrogen bonds : bond 0.03374 ( 536) hydrogen bonds : angle 5.74014 ( 1515) *********************** 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 246 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.6257 (mt-10) cc_final: 0.5888 (tt0) REVERT: C 24 CYS cc_start: 0.5175 (t) cc_final: 0.4925 (t) REVERT: D 163 TRP cc_start: 0.6306 (m100) cc_final: 0.5954 (m-10) REVERT: D 180 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.5735 (mttt) REVERT: d 44 VAL cc_start: 0.5418 (OUTLIER) cc_final: 0.5120 (t) REVERT: e 121 ASN cc_start: 0.7019 (t0) cc_final: 0.6748 (t0) REVERT: e 145 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.3323 (pp) REVERT: f 111 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.6179 (t80) REVERT: f 149 TYR cc_start: 0.5452 (OUTLIER) cc_final: 0.4774 (t80) outliers start: 72 outliers final: 41 residues processed: 230 average time/residue: 0.0798 time to fit residues: 28.5417 Evaluate side-chains 210 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 93 ASN Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 57 VAL 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 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 D residue 205 ASN 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 122 CYS Chi-restraints excluded: chain e residue 145 LEU 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 94 SER 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 17 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 50 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 69 optimal weight: 0.1980 chunk 5 optimal weight: 0.0010 chunk 112 optimal weight: 0.9980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.214463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.182594 restraints weight = 13194.420| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.78 r_work: 0.4095 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1901 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= 0.134 Angle : 0.575 6.769 14569 Z= 0.298 Chirality : 0.042 0.198 1704 Planarity : 0.004 0.045 1804 Dihedral : 5.776 56.806 1480 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.25 % Allowed : 24.82 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.23), residues: 1330 helix: 1.49 (0.30), residues: 272 sheet: 0.04 (0.24), residues: 467 loop : -0.58 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 82 TYR 0.021 0.001 TYR A 72 PHE 0.013 0.001 PHE A 141 TRP 0.010 0.001 TRP D 47 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00304 (10685) covalent geometry : angle 0.57462 (14535) SS BOND : bond 0.00230 ( 17) SS BOND : angle 0.72838 ( 34) hydrogen bonds : bond 0.03100 ( 536) hydrogen bonds : angle 5.42281 ( 1515) *********************** 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 244 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 173 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: C 24 CYS cc_start: 0.5049 (t) cc_final: 0.4829 (t) REVERT: C 152 ILE cc_start: 0.4948 (OUTLIER) cc_final: 0.4516 (tt) REVERT: D 163 TRP cc_start: 0.6384 (m100) cc_final: 0.6060 (m-10) REVERT: d 45 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5799 (tm-30) REVERT: e 56 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6654 (tp30) REVERT: f 111 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.6287 (t80) REVERT: f 149 TYR cc_start: 0.5520 (OUTLIER) cc_final: 0.4783 (t80) REVERT: g 61 MET cc_start: 0.6307 (tpp) cc_final: 0.6086 (tpp) outliers start: 71 outliers final: 45 residues processed: 230 average time/residue: 0.0834 time to fit residues: 29.4504 Evaluate side-chains 211 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain A residue 134 VAL 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 87 THR Chi-restraints excluded: chain B residue 89 GLU 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 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 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 179 LEU 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 46 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 45 GLU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 ASN C 200 HIS C 212 ASN f 61 HIS f 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.205647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.165426 restraints weight = 13295.609| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.53 r_work: 0.4007 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2590 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= 0.215 Angle : 0.650 7.401 14569 Z= 0.338 Chirality : 0.045 0.230 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.740 59.371 1473 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 7.22 % Allowed : 25.44 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1330 helix: 1.62 (0.30), residues: 272 sheet: -0.25 (0.24), residues: 466 loop : -0.72 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 102 TYR 0.023 0.002 TYR C 87 PHE 0.020 0.002 PHE A 99 TRP 0.017 0.002 TRP C 36 HIS 0.005 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00492 (10685) covalent geometry : angle 0.64938 (14535) SS BOND : bond 0.00497 ( 17) SS BOND : angle 0.86995 ( 34) hydrogen bonds : bond 0.03384 ( 536) hydrogen bonds : angle 5.59697 ( 1515) *********************** 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 246 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 164 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 ILE cc_start: 0.4978 (OUTLIER) cc_final: 0.4711 (tt) REVERT: D 163 TRP cc_start: 0.6672 (m100) cc_final: 0.6147 (m-10) REVERT: D 180 LYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6061 (mttm) REVERT: e 56 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6907 (tp30) REVERT: e 121 ASN cc_start: 0.7528 (t0) cc_final: 0.7306 (t0) REVERT: f 111 TYR cc_start: 0.7272 (OUTLIER) cc_final: 0.6751 (t80) REVERT: f 149 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.5021 (t80) outliers start: 82 outliers final: 58 residues processed: 227 average time/residue: 0.0831 time to fit residues: 29.1237 Evaluate side-chains 216 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 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 138 LEU 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 71 THR Chi-restraints excluded: chain D residue 84 LEU 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 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 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 112 LEU 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 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 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 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.208355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.164940 restraints weight = 13147.418| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.34 r_work: 0.4051 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2687 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= 0.153 Angle : 0.597 6.863 14569 Z= 0.308 Chirality : 0.043 0.207 1704 Planarity : 0.004 0.047 1804 Dihedral : 5.434 59.063 1470 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.60 % Allowed : 26.58 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1330 helix: 1.85 (0.30), residues: 273 sheet: -0.25 (0.23), residues: 465 loop : -0.69 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 102 TYR 0.021 0.002 TYR A 72 PHE 0.019 0.002 PHE m 264 TRP 0.014 0.002 TRP B 163 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00352 (10685) covalent geometry : angle 0.59698 (14535) SS BOND : bond 0.00282 ( 17) SS BOND : angle 0.70055 ( 34) hydrogen bonds : bond 0.03051 ( 536) hydrogen bonds : angle 5.34408 ( 1515) *********************** 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: 75 poor density : 164 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6647 (m100) cc_final: 0.6107 (m-10) REVERT: D 180 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6404 (mttm) REVERT: e 56 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: e 121 ASN cc_start: 0.7649 (t0) cc_final: 0.7378 (t0) REVERT: f 96 TYR cc_start: 0.8372 (m-80) cc_final: 0.7817 (m-80) REVERT: f 111 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6850 (t80) REVERT: f 149 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.4987 (t80) outliers start: 75 outliers final: 54 residues processed: 225 average time/residue: 0.0748 time to fit residues: 26.0420 Evaluate side-chains 212 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 A residue 208 VAL 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 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 93 ASN 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 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU 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 D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 65 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 32 optimal weight: 0.0370 chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.207774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.164112 restraints weight = 13272.552| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.35 r_work: 0.4042 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2854 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= 0.155 Angle : 0.605 9.677 14569 Z= 0.310 Chirality : 0.043 0.224 1704 Planarity : 0.004 0.048 1804 Dihedral : 5.392 59.520 1470 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 6.95 % Allowed : 26.94 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.22), residues: 1330 helix: 1.98 (0.30), residues: 273 sheet: -0.25 (0.23), residues: 474 loop : -0.67 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 102 TYR 0.023 0.002 TYR A 72 PHE 0.014 0.002 PHE A 99 TRP 0.019 0.002 TRP B 163 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00358 (10685) covalent geometry : angle 0.60508 (14535) SS BOND : bond 0.00309 ( 17) SS BOND : angle 0.69144 ( 34) hydrogen bonds : bond 0.03005 ( 536) hydrogen bonds : angle 5.28885 ( 1515) *********************** 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 238 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 159 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6668 (m100) cc_final: 0.6143 (m-10) REVERT: D 180 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6399 (mttt) REVERT: e 56 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: e 121 ASN cc_start: 0.7586 (t0) cc_final: 0.7235 (t0) REVERT: f 96 TYR cc_start: 0.8229 (m-80) cc_final: 0.7695 (m-80) REVERT: f 111 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6648 (t80) REVERT: f 149 TYR cc_start: 0.5435 (OUTLIER) cc_final: 0.4808 (t80) outliers start: 79 outliers final: 64 residues processed: 219 average time/residue: 0.0735 time to fit residues: 25.1709 Evaluate side-chains 222 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 154 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 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 70 LEU 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 28 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 93 ASN 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 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU 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 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 41 ILE 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 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 123 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 128 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4599 r_free = 0.4599 target = 0.205669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.162432 restraints weight = 13234.632| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.26 r_work: 0.4023 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10702 Z= 0.191 Angle : 0.636 10.412 14569 Z= 0.326 Chirality : 0.044 0.247 1704 Planarity : 0.004 0.048 1804 Dihedral : 5.518 58.013 1470 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 7.13 % Allowed : 26.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.22), residues: 1330 helix: 1.98 (0.30), residues: 272 sheet: -0.37 (0.23), residues: 476 loop : -0.75 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 102 TYR 0.020 0.002 TYR A 72 PHE 0.018 0.002 PHE A 99 TRP 0.018 0.002 TRP B 163 HIS 0.003 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00441 (10685) covalent geometry : angle 0.63539 (14535) SS BOND : bond 0.00380 ( 17) SS BOND : angle 0.77176 ( 34) hydrogen bonds : bond 0.03136 ( 536) hydrogen bonds : angle 5.39868 ( 1515) *********************** 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 242 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 161 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6784 (m100) cc_final: 0.6515 (m100) REVERT: D 180 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6460 (mttt) REVERT: d 98 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7676 (tt0) REVERT: e 56 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: e 121 ASN cc_start: 0.7715 (t0) cc_final: 0.7389 (t0) REVERT: f 96 TYR cc_start: 0.8425 (m-80) cc_final: 0.7839 (m-80) REVERT: f 111 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6983 (t80) REVERT: f 149 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.4884 (t80) outliers start: 81 outliers final: 65 residues processed: 228 average time/residue: 0.0773 time to fit residues: 27.7070 Evaluate side-chains 226 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 157 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 LEU 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 6 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 34 LEU 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 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU 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 D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 65 LEU 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 123 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.206362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.163484 restraints weight = 13248.712| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.27 r_work: 0.4036 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10702 Z= 0.175 Angle : 0.641 11.371 14569 Z= 0.327 Chirality : 0.044 0.271 1704 Planarity : 0.004 0.082 1804 Dihedral : 5.514 57.653 1470 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 7.22 % Allowed : 26.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1330 helix: 2.04 (0.30), residues: 272 sheet: -0.44 (0.23), residues: 473 loop : -0.77 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 102 TYR 0.019 0.002 TYR A 72 PHE 0.016 0.002 PHE A 99 TRP 0.018 0.002 TRP B 163 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00408 (10685) covalent geometry : angle 0.64027 (14535) SS BOND : bond 0.00326 ( 17) SS BOND : angle 0.79702 ( 34) hydrogen bonds : bond 0.03044 ( 536) hydrogen bonds : angle 5.36067 ( 1515) *********************** 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: 82 poor density : 159 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: C 24 CYS cc_start: 0.5647 (t) cc_final: 0.5356 (t) REVERT: D 163 TRP cc_start: 0.6793 (m100) cc_final: 0.6483 (m100) REVERT: D 180 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6455 (mttt) REVERT: d 98 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7684 (tt0) REVERT: e 56 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: e 121 ASN cc_start: 0.7765 (t0) cc_final: 0.7451 (t0) REVERT: f 96 TYR cc_start: 0.8392 (m-80) cc_final: 0.7815 (m-80) REVERT: f 111 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.6967 (t80) REVERT: f 149 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.4835 (t80) outliers start: 82 outliers final: 67 residues processed: 224 average time/residue: 0.0703 time to fit residues: 24.7150 Evaluate side-chains 226 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 155 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 LEU 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 28 GLN 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 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 41 HIS Chi-restraints excluded: chain D residue 69 THR 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 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 D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 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 e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 123 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 113 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 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 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.206510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.167532 restraints weight = 13220.579| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.34 r_work: 0.4036 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3264 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= 0.175 Angle : 0.645 11.906 14569 Z= 0.328 Chirality : 0.044 0.282 1704 Planarity : 0.004 0.075 1804 Dihedral : 5.504 57.662 1470 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.60 % Allowed : 27.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1330 helix: 2.08 (0.30), residues: 272 sheet: -0.44 (0.23), residues: 468 loop : -0.77 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.023 0.002 TYR A 72 PHE 0.016 0.002 PHE A 99 TRP 0.018 0.002 TRP B 163 HIS 0.002 0.001 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00407 (10685) covalent geometry : angle 0.64500 (14535) SS BOND : bond 0.00352 ( 17) SS BOND : angle 0.78007 ( 34) hydrogen bonds : bond 0.03018 ( 536) hydrogen bonds : angle 5.35176 ( 1515) *********************** 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 230 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 155 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: C 24 CYS cc_start: 0.5634 (t) cc_final: 0.5391 (t) REVERT: D 163 TRP cc_start: 0.6696 (m100) cc_final: 0.6342 (m100) REVERT: D 180 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6414 (mttt) REVERT: d 98 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7729 (tt0) REVERT: e 56 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6989 (tp30) REVERT: e 121 ASN cc_start: 0.7794 (t0) cc_final: 0.7488 (t0) REVERT: f 96 TYR cc_start: 0.8388 (m-80) cc_final: 0.7851 (m-80) REVERT: f 111 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6976 (t80) REVERT: f 149 TYR cc_start: 0.5279 (OUTLIER) cc_final: 0.4671 (t80) outliers start: 75 outliers final: 68 residues processed: 215 average time/residue: 0.0773 time to fit residues: 26.1842 Evaluate side-chains 227 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 155 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 LEU 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 28 GLN Chi-restraints excluded: chain C residue 34 LEU 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 41 HIS Chi-restraints excluded: chain D residue 69 THR 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 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 D residue 204 CYS Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 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 e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 123 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.206756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.167770 restraints weight = 13182.834| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.35 r_work: 0.4031 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10702 Z= 0.171 Angle : 0.641 11.858 14569 Z= 0.326 Chirality : 0.044 0.291 1704 Planarity : 0.004 0.072 1804 Dihedral : 5.489 57.208 1470 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 6.51 % Allowed : 27.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1330 helix: 2.12 (0.30), residues: 272 sheet: -0.45 (0.23), residues: 475 loop : -0.77 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 102 TYR 0.019 0.002 TYR A 72 PHE 0.026 0.002 PHE m 264 TRP 0.019 0.002 TRP B 163 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00397 (10685) covalent geometry : angle 0.64109 (14535) SS BOND : bond 0.00314 ( 17) SS BOND : angle 0.75675 ( 34) hydrogen bonds : bond 0.02994 ( 536) hydrogen bonds : angle 5.32570 ( 1515) ********************** 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 228 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 154 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: C 24 CYS cc_start: 0.5369 (t) cc_final: 0.5134 (t) REVERT: D 101 TYR cc_start: 0.7864 (t80) cc_final: 0.7642 (t80) REVERT: D 154 TYR cc_start: 0.5686 (p90) cc_final: 0.5419 (p90) REVERT: D 163 TRP cc_start: 0.6701 (m100) cc_final: 0.6432 (m100) REVERT: D 180 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6423 (mttt) REVERT: d 98 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7586 (tt0) REVERT: e 56 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6895 (tp30) REVERT: f 96 TYR cc_start: 0.8260 (m-80) cc_final: 0.7707 (m-80) REVERT: f 111 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6787 (t80) REVERT: f 149 TYR cc_start: 0.5211 (OUTLIER) cc_final: 0.4703 (t80) outliers start: 74 outliers final: 65 residues processed: 214 average time/residue: 0.0794 time to fit residues: 26.8177 Evaluate side-chains 220 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 151 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 70 LEU 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 53 SER 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 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 69 THR 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 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 D residue 204 CYS Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 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 e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 123 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 191 HIS C 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.205791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.166817 restraints weight = 13373.846| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.27 r_work: 0.4031 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3886 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3483 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= 0.189 Angle : 0.659 11.610 14569 Z= 0.337 Chirality : 0.045 0.288 1704 Planarity : 0.004 0.071 1804 Dihedral : 5.581 56.977 1470 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.60 % Allowed : 27.64 % Favored : 65.76 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1330 helix: 2.07 (0.30), residues: 272 sheet: -0.51 (0.23), residues: 475 loop : -0.78 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG g 102 TYR 0.017 0.002 TYR D 108 PHE 0.017 0.002 PHE A 99 TRP 0.019 0.002 TRP B 163 HIS 0.010 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00439 (10685) covalent geometry : angle 0.65882 (14535) SS BOND : bond 0.00358 ( 17) SS BOND : angle 0.78596 ( 34) hydrogen bonds : bond 0.03069 ( 536) hydrogen bonds : angle 5.39816 ( 1515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4507.36 seconds wall clock time: 77 minutes 40.91 seconds (4660.91 seconds total)