Starting phenix.real_space_refine on Fri Feb 14 16:51:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci8_45614/02_2025/9ci8_45614.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci8_45614/02_2025/9ci8_45614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ci8_45614/02_2025/9ci8_45614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci8_45614/02_2025/9ci8_45614.map" model { file = "/net/cci-nas-00/data/ceres_data/9ci8_45614/02_2025/9ci8_45614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci8_45614/02_2025/9ci8_45614.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6698 2.51 5 N 1693 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10466 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1496 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 196} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1491 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 183} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1513 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1557 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "b" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 248 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 643 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "e" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "f" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 972 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 795 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "m" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 7.86, per 1000 atoms: 0.75 Number of scatterers: 10466 At special positions: 0 Unit cell: (77.9, 173.02, 164.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2009 8.00 N 1693 7.00 C 6698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.3 seconds 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2582 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 27 sheets defined 22.1% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.671A pdb=" N ILE A 84 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.811A pdb=" N HIS C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.828A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 55 removed outlier: 3.727A pdb=" N PHE a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 56 Processing helix chain 'd' and resid 100 through 126 Processing helix chain 'e' and resid 88 through 93 removed outlier: 3.877A pdb=" N SER e 93 " --> pdb=" O GLU e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 154 removed outlier: 3.901A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 93 removed outlier: 3.828A pdb=" N SER f 93 " --> pdb=" O GLU f 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 155 removed outlier: 3.657A pdb=" N SER f 152 " --> pdb=" O VAL f 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 25 through 29 removed outlier: 3.733A pdb=" N ASN g 28 " --> pdb=" O ILE g 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS g 29 " --> pdb=" O LYS g 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 25 through 29' Processing helix chain 'g' and resid 78 through 80 No H-bonds generated for 'chain 'g' and resid 78 through 80' Processing helix chain 'g' and resid 111 through 135 Processing helix chain 'm' and resid 239 through 271 Processing helix chain 'n' and resid 242 through 278 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.578A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 120 removed outlier: 4.010A pdb=" N ASN A 139 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER A 133 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU A 183 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL A 135 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 181 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE A 137 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER A 179 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN A 139 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET A 177 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 176 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 157 removed outlier: 4.395A pdb=" N TRP A 150 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 196 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 209 " --> pdb=" O CYS A 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 207 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.503A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET B 34 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.830A pdb=" N TYR B 184 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 129 through 133 removed outlier: 5.830A pdb=" N TYR B 184 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AB1, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.545A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 120 removed outlier: 5.759A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 147 through 151 removed outlier: 3.560A pdb=" N LYS C 209 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.558A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.431A pdb=" N CYS D 96 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP D 112 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG D 98 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.394A pdb=" N TYR D 184 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 133 removed outlier: 6.394A pdb=" N TYR D 184 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 160 through 163 removed outlier: 3.540A pdb=" N THR D 160 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 26 through 29 removed outlier: 5.824A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 42 through 46 removed outlier: 5.153A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG e 115 " --> pdb=" O HIS d 89 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AC5, first strand: chain 'e' and resid 37 through 40 Processing sheet with id=AC6, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AC7, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.819A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS g 57 " --> pdb=" O MET g 61 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N MET g 61 " --> pdb=" O LYS g 57 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AC9, first strand: chain 'g' and resid 31 through 33 removed outlier: 7.309A pdb=" N VAL g 42 " --> pdb=" O LEU g 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU g 74 " --> pdb=" O VAL g 42 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 3.23 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.350 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- 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 10685 Z= 0.235 Angle : 0.803 14.739 14535 Z= 0.421 Chirality : 0.049 0.278 1704 Planarity : 0.005 0.051 1804 Dihedral : 16.954 85.653 3704 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.93 % Allowed : 27.38 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1330 helix: -0.49 (0.28), residues: 266 sheet: -0.03 (0.24), residues: 455 loop : -0.89 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 97 HIS 0.007 0.001 HIS d 89 PHE 0.029 0.002 PHE A 141 TYR 0.053 0.002 TYR n 253 ARG 0.007 0.001 ARG g 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2660 Ramachandran restraints generated. 1330 Oldfield, 0 Emsley, 1330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6093 (m100) cc_final: 0.5751 (m-10) REVERT: d 44 VAL cc_start: 0.5438 (OUTLIER) cc_final: 0.5233 (t) REVERT: e 56 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6543 (tp30) REVERT: e 121 ASN cc_start: 0.6676 (t0) cc_final: 0.6339 (t0) REVERT: e 145 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3136 (pp) REVERT: f 96 TYR cc_start: 0.8023 (m-80) cc_final: 0.7591 (m-80) REVERT: f 111 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.5934 (t80) REVERT: f 149 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.4242 (t80) REVERT: g 84 MET cc_start: 0.3717 (mmm) cc_final: 0.2926 (ttm) REVERT: n 253 TYR cc_start: 0.7683 (m-80) cc_final: 0.7357 (m-80) outliers start: 56 outliers final: 24 residues processed: 263 average time/residue: 0.2075 time to fit residues: 78.5541 Evaluate side-chains 198 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 99 LEU Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 55 SER Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN C 212 ASN f 61 HIS f 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.210380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.177644 restraints weight = 13020.815| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.67 r_work: 0.4051 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10685 Z= 0.295 Angle : 0.636 7.556 14535 Z= 0.334 Chirality : 0.044 0.203 1704 Planarity : 0.005 0.049 1804 Dihedral : 7.067 59.150 1509 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 7.31 % Allowed : 24.47 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1330 helix: 0.73 (0.30), residues: 272 sheet: -0.13 (0.24), residues: 469 loop : -0.76 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 47 HIS 0.004 0.001 HIS f 61 PHE 0.019 0.002 PHE A 99 TYR 0.021 0.002 TYR A 72 ARG 0.003 0.001 ARG D 98 *********************** 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 251 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 168 time to evaluate : 1.160 Fit side-chains REVERT: A 80 GLU cc_start: 0.6304 (mt-10) cc_final: 0.5939 (tt0) REVERT: C 24 CYS cc_start: 0.5203 (t) cc_final: 0.4968 (t) REVERT: D 163 TRP cc_start: 0.6324 (m100) cc_final: 0.5940 (m-10) REVERT: D 180 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.5742 (mttt) REVERT: d 44 VAL cc_start: 0.5387 (OUTLIER) cc_final: 0.5100 (t) REVERT: e 56 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6703 (tp30) REVERT: e 121 ASN cc_start: 0.7166 (t0) cc_final: 0.6839 (t0) REVERT: f 111 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6419 (t80) REVERT: f 149 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.4799 (t80) outliers start: 83 outliers final: 47 residues processed: 237 average time/residue: 0.1721 time to fit residues: 62.5367 Evaluate side-chains 213 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 44 VAL Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 243 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 93 optimal weight: 0.0570 chunk 118 optimal weight: 0.0970 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 200 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 = 0.4710 r_free = 0.4710 target = 0.213277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.182886 restraints weight = 13206.953| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.44 r_work: 0.4127 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10685 Z= 0.177 Angle : 0.561 6.802 14535 Z= 0.292 Chirality : 0.042 0.192 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.886 55.910 1482 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.84 % Allowed : 27.46 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1330 helix: 1.50 (0.30), residues: 272 sheet: 0.02 (0.24), residues: 467 loop : -0.61 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.003 0.001 HIS d 89 PHE 0.013 0.001 PHE A 141 TYR 0.022 0.001 TYR A 72 ARG 0.003 0.000 ARG m 253 *********************** 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 231 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 1.182 Fit side-chains REVERT: A 80 GLU cc_start: 0.6166 (mt-10) cc_final: 0.5838 (tt0) REVERT: C 24 CYS cc_start: 0.5085 (t) cc_final: 0.4845 (t) REVERT: C 152 ILE cc_start: 0.4919 (OUTLIER) cc_final: 0.4596 (tt) REVERT: D 163 TRP cc_start: 0.6400 (m100) cc_final: 0.5934 (m-10) REVERT: d 44 VAL cc_start: 0.5305 (OUTLIER) cc_final: 0.4944 (t) REVERT: d 45 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5554 (tm-30) REVERT: f 111 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6252 (t80) REVERT: f 149 TYR cc_start: 0.5461 (OUTLIER) cc_final: 0.4721 (t80) outliers start: 55 outliers final: 32 residues processed: 217 average time/residue: 0.1864 time to fit residues: 60.9649 Evaluate side-chains 198 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 81 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 16 LEU 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 152 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 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 45 GLU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 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 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 105 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4611 r_free = 0.4611 target = 0.208025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.161521 restraints weight = 12830.682| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.49 r_work: 0.3997 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10685 Z= 0.382 Angle : 0.684 7.678 14535 Z= 0.357 Chirality : 0.046 0.237 1704 Planarity : 0.005 0.048 1804 Dihedral : 5.797 58.311 1471 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 7.22 % Allowed : 26.23 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1330 helix: 1.59 (0.30), residues: 272 sheet: -0.30 (0.23), residues: 467 loop : -0.79 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 36 HIS 0.004 0.001 HIS D 173 PHE 0.023 0.002 PHE A 99 TYR 0.026 0.002 TYR C 87 ARG 0.005 0.001 ARG g 102 *********************** 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 240 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 158 time to evaluate : 1.193 Fit side-chains REVERT: A 78 ASN cc_start: 0.6430 (p0) cc_final: 0.6076 (p0) REVERT: A 80 GLU cc_start: 0.5992 (mt-10) cc_final: 0.5313 (tt0) REVERT: C 152 ILE cc_start: 0.5092 (OUTLIER) cc_final: 0.4832 (tt) REVERT: D 180 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6043 (mttt) REVERT: D 185 THR cc_start: 0.6875 (OUTLIER) cc_final: 0.6661 (p) REVERT: d 98 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7434 (tt0) REVERT: e 56 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: e 121 ASN cc_start: 0.7585 (t0) cc_final: 0.7292 (t0) REVERT: f 111 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6866 (t80) REVERT: f 149 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5190 (t80) outliers start: 82 outliers final: 57 residues processed: 220 average time/residue: 0.1779 time to fit residues: 59.8630 Evaluate side-chains 213 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 150 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 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 152 ILE Chi-restraints excluded: chain C residue 182 THR 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 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 D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 115 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.208375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165152 restraints weight = 13123.092| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.35 r_work: 0.4048 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10685 Z= 0.212 Angle : 0.592 7.183 14535 Z= 0.306 Chirality : 0.043 0.198 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.440 59.310 1470 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.55 % Allowed : 27.82 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1330 helix: 1.89 (0.30), residues: 272 sheet: -0.29 (0.23), residues: 468 loop : -0.70 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 163 HIS 0.003 0.001 HIS d 89 PHE 0.034 0.002 PHE m 264 TYR 0.014 0.001 TYR C 142 ARG 0.003 0.000 ARG m 253 *********************** 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 228 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 1.129 Fit side-chains REVERT: A 78 ASN cc_start: 0.6460 (p0) cc_final: 0.6170 (p0) REVERT: A 80 GLU cc_start: 0.5879 (mt-10) cc_final: 0.5344 (tt0) REVERT: D 163 TRP cc_start: 0.7013 (m100) cc_final: 0.6380 (m100) REVERT: D 180 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6092 (mttt) REVERT: e 56 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6890 (tp30) REVERT: e 121 ASN cc_start: 0.7567 (t0) cc_final: 0.7304 (t0) REVERT: f 96 TYR cc_start: 0.8198 (m-80) cc_final: 0.7607 (m-80) REVERT: f 111 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6752 (t80) REVERT: f 149 TYR cc_start: 0.5620 (OUTLIER) cc_final: 0.4924 (t80) outliers start: 63 outliers final: 45 residues processed: 214 average time/residue: 0.1840 time to fit residues: 59.9581 Evaluate side-chains 203 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 103 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 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 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 69 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 180 LYS Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain 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 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 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4612 r_free = 0.4612 target = 0.207082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.163304 restraints weight = 13275.813| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 2.37 r_work: 0.4028 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10685 Z= 0.246 Angle : 0.615 9.340 14535 Z= 0.315 Chirality : 0.043 0.255 1704 Planarity : 0.004 0.048 1804 Dihedral : 5.426 58.868 1470 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.51 % Allowed : 27.73 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1330 helix: 1.93 (0.30), residues: 272 sheet: -0.33 (0.23), residues: 473 loop : -0.65 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 163 HIS 0.002 0.001 HIS C 191 PHE 0.015 0.002 PHE A 99 TYR 0.015 0.002 TYR C 87 ARG 0.002 0.000 ARG g 102 *********************** 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 236 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 162 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6847 (m100) cc_final: 0.6196 (m-10) REVERT: D 180 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6350 (mttm) REVERT: e 56 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6963 (tp30) REVERT: e 121 ASN cc_start: 0.7564 (t0) cc_final: 0.7286 (t0) REVERT: f 111 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6755 (t80) REVERT: f 149 TYR cc_start: 0.5553 (OUTLIER) cc_final: 0.4924 (t80) outliers start: 74 outliers final: 56 residues processed: 222 average time/residue: 0.1747 time to fit residues: 59.2139 Evaluate side-chains 213 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU 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 34 LEU Chi-restraints excluded: chain C residue 76 ILE 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 35 ASN Chi-restraints excluded: chain D residue 37 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 180 LYS Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 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 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 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 99 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.207644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.164123 restraints weight = 13241.385| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 2.34 r_work: 0.4039 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10685 Z= 0.225 Angle : 0.608 10.863 14535 Z= 0.311 Chirality : 0.043 0.233 1704 Planarity : 0.004 0.047 1804 Dihedral : 5.370 58.992 1470 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 6.78 % Allowed : 27.46 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1330 helix: 2.05 (0.30), residues: 272 sheet: -0.33 (0.23), residues: 473 loop : -0.64 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 163 HIS 0.004 0.001 HIS A 191 PHE 0.019 0.001 PHE m 264 TYR 0.014 0.001 TYR B 108 ARG 0.002 0.000 ARG m 253 *********************** 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 235 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 158 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6828 (m100) cc_final: 0.6197 (m-10) REVERT: D 180 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6368 (mttt) REVERT: d 98 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7480 (tt0) REVERT: e 56 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: e 121 ASN cc_start: 0.7577 (t0) cc_final: 0.7287 (t0) REVERT: f 96 TYR cc_start: 0.8192 (m-80) cc_final: 0.7638 (m-80) REVERT: f 111 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6672 (t80) REVERT: f 149 TYR cc_start: 0.5425 (OUTLIER) cc_final: 0.4801 (t80) outliers start: 77 outliers final: 60 residues processed: 221 average time/residue: 0.1784 time to fit residues: 60.0147 Evaluate side-chains 220 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 53 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 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 98 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 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 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 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 92 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 105 optimal weight: 0.0970 chunk 113 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.210489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.167744 restraints weight = 13180.612| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.37 r_work: 0.4075 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10685 Z= 0.184 Angle : 0.603 11.534 14535 Z= 0.304 Chirality : 0.043 0.248 1704 Planarity : 0.004 0.047 1804 Dihedral : 5.251 59.095 1470 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.81 % Allowed : 28.35 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1330 helix: 2.28 (0.30), residues: 271 sheet: -0.29 (0.23), residues: 462 loop : -0.62 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 163 HIS 0.003 0.001 HIS A 191 PHE 0.012 0.001 PHE A 211 TYR 0.011 0.001 TYR D 102 ARG 0.003 0.000 ARG m 253 *********************** 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 227 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: D 163 TRP cc_start: 0.6766 (m100) cc_final: 0.6182 (m-10) REVERT: D 180 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6370 (mttt) REVERT: e 121 ASN cc_start: 0.7555 (t0) cc_final: 0.7311 (t0) REVERT: f 96 TYR cc_start: 0.8105 (m-80) cc_final: 0.7565 (m-80) REVERT: f 111 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6506 (t80) REVERT: f 149 TYR cc_start: 0.5422 (OUTLIER) cc_final: 0.4813 (t80) outliers start: 66 outliers final: 52 residues processed: 215 average time/residue: 0.1820 time to fit residues: 58.7008 Evaluate side-chains 210 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 155 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 76 ILE 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 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 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 b residue 41 ILE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.203991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.162392 restraints weight = 13436.947| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.48 r_work: 0.3983 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10685 Z= 0.365 Angle : 0.703 11.608 14535 Z= 0.360 Chirality : 0.046 0.291 1704 Planarity : 0.004 0.049 1804 Dihedral : 5.662 55.699 1470 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 6.51 % Allowed : 28.26 % Favored : 65.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1330 helix: 2.07 (0.30), residues: 271 sheet: -0.50 (0.23), residues: 475 loop : -0.83 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 36 HIS 0.003 0.001 HIS A 191 PHE 0.023 0.002 PHE A 99 TYR 0.021 0.002 TYR C 87 ARG 0.010 0.001 ARG g 82 *********************** 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: 74 poor density : 156 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: D 101 TYR cc_start: 0.7991 (t80) cc_final: 0.7695 (t80) REVERT: D 163 TRP cc_start: 0.6916 (m100) cc_final: 0.6419 (m100) REVERT: D 180 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6424 (mttt) REVERT: d 98 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7504 (tm-30) REVERT: e 56 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: f 111 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6957 (t80) REVERT: f 149 TYR cc_start: 0.5415 (OUTLIER) cc_final: 0.4767 (t80) outliers start: 74 outliers final: 61 residues processed: 213 average time/residue: 0.1811 time to fit residues: 58.3252 Evaluate side-chains 218 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 153 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 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 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 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 76 ILE 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 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 98 ARG Chi-restraints excluded: chain D residue 116 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 b residue 41 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 127 VAL Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 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 m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.206911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.165716 restraints weight = 13228.152| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.53 r_work: 0.4018 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10685 Z= 0.249 Angle : 0.650 12.049 14535 Z= 0.330 Chirality : 0.044 0.278 1704 Planarity : 0.004 0.090 1804 Dihedral : 5.509 56.811 1470 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.46 % Allowed : 29.31 % Favored : 65.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1330 helix: 2.11 (0.30), residues: 272 sheet: -0.52 (0.23), residues: 471 loop : -0.73 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 163 HIS 0.003 0.001 HIS d 89 PHE 0.031 0.002 PHE m 264 TYR 0.014 0.002 TYR D 108 ARG 0.008 0.000 ARG g 82 ********************** 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 215 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.7073 (mmm) cc_final: 0.6858 (mmm) REVERT: D 101 TYR cc_start: 0.7919 (t80) cc_final: 0.7670 (t80) REVERT: D 163 TRP cc_start: 0.6851 (m100) cc_final: 0.6349 (m-10) REVERT: D 180 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6418 (mttt) REVERT: d 98 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7437 (tm-30) REVERT: e 56 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: f 111 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6782 (t80) REVERT: f 149 TYR cc_start: 0.5402 (OUTLIER) cc_final: 0.4776 (t80) outliers start: 62 outliers final: 56 residues processed: 202 average time/residue: 0.1718 time to fit residues: 53.1661 Evaluate side-chains 214 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 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 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 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 76 ILE 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 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 98 ARG Chi-restraints excluded: chain D residue 116 THR 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 b residue 41 ILE Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 111 ASP Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 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 m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.205677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164321 restraints weight = 13221.211| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.47 r_work: 0.4003 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10685 Z= 0.285 Angle : 0.661 11.744 14535 Z= 0.336 Chirality : 0.045 0.277 1704 Planarity : 0.004 0.080 1804 Dihedral : 5.562 56.288 1470 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.72 % Allowed : 29.14 % Favored : 65.14 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1330 helix: 2.12 (0.30), residues: 271 sheet: -0.53 (0.23), residues: 475 loop : -0.77 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 163 HIS 0.008 0.001 HIS C 191 PHE 0.017 0.002 PHE A 99 TYR 0.017 0.002 TYR D 108 ARG 0.008 0.001 ARG g 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8027.74 seconds wall clock time: 143 minutes 17.51 seconds (8597.51 seconds total)