Starting phenix.real_space_refine on Wed Sep 25 13:28:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ci8_45614/09_2024/9ci8_45614.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ci8_45614/09_2024/9ci8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ci8_45614/09_2024/9ci8_45614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ci8_45614/09_2024/9ci8_45614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ci8_45614/09_2024/9ci8_45614.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ci8_45614/09_2024/9ci8_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-5461/modules/chem_data/mon_lib" Total number of atoms: 10466 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1496 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 196} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1491 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 183} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1513 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1557 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "b" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 248 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 643 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "e" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "f" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 972 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 795 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "m" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 281 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 8.05, per 1000 atoms: 0.77 Number of scatterers: 10466 At special positions: 0 Unit cell: (77.9, 173.02, 164.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2009 8.00 N 1693 7.00 C 6698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 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: 1.46 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: 3.31 Time building geometry restraints manager: 3.07 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: 19.010 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.300 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.280 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 56 poor density : 223 time to evaluate : 1.056 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: 0.2031 time to fit residues: 76.8059 Evaluate side-chains 198 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 fitting. rotamer outliers: 83 poor density : 168 time to evaluate : 1.191 Fit side-chains REVERT: A 80 GLU cc_start: 0.6188 (mt-10) cc_final: 0.5856 (tt0) REVERT: C 24 CYS cc_start: 0.5348 (t) cc_final: 0.5069 (t) REVERT: D 163 TRP cc_start: 0.6326 (m100) cc_final: 0.5976 (m-10) REVERT: D 180 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.5766 (mttt) REVERT: d 44 VAL cc_start: 0.5166 (OUTLIER) cc_final: 0.4926 (t) REVERT: e 56 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6827 (tp30) REVERT: e 121 ASN cc_start: 0.7093 (t0) cc_final: 0.6807 (t0) REVERT: f 111 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6351 (t80) REVERT: f 149 TYR cc_start: 0.4846 (OUTLIER) cc_final: 0.4382 (t80) outliers start: 83 outliers final: 47 residues processed: 237 average time/residue: 0.1726 time to fit residues: 62.1908 Evaluate side-chains 213 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 161 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 66 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 96 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2208 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= 0.248 Angle : 0.603 6.885 14535 Z= 0.313 Chirality : 0.044 0.210 1704 Planarity : 0.004 0.045 1804 Dihedral : 6.112 57.720 1482 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.90 % Allowed : 26.58 % Favored : 67.52 % 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: -0.15 (0.22), residues: 1330 helix: 1.39 (0.30), residues: 272 sheet: -0.10 (0.24), residues: 469 loop : -0.73 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 47 HIS 0.003 0.001 HIS B 208 PHE 0.015 0.002 PHE A 99 TYR 0.023 0.002 TYR A 72 ARG 0.003 0.000 ARG g 102 *********************** 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 237 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 170 time to evaluate : 1.248 Fit side-chains REVERT: A 80 GLU cc_start: 0.6197 (mt-10) cc_final: 0.5825 (tt0) REVERT: C 24 CYS cc_start: 0.5244 (t) cc_final: 0.4981 (t) REVERT: C 152 ILE cc_start: 0.4978 (OUTLIER) cc_final: 0.4668 (tt) REVERT: D 163 TRP cc_start: 0.6477 (m100) cc_final: 0.6062 (m-10) REVERT: e 56 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: f 111 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6513 (t80) REVERT: f 149 TYR cc_start: 0.4885 (OUTLIER) cc_final: 0.4305 (t80) outliers start: 67 outliers final: 47 residues processed: 222 average time/residue: 0.1772 time to fit residues: 59.3202 Evaluate side-chains 210 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 159 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 105 LEU 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 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 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 136 VAL Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10685 Z= 0.229 Angle : 0.588 6.868 14535 Z= 0.305 Chirality : 0.043 0.205 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.814 58.823 1477 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.87 % Allowed : 26.67 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1330 helix: 1.76 (0.30), residues: 272 sheet: -0.17 (0.23), residues: 477 loop : -0.67 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 47 HIS 0.002 0.001 HIS C 191 PHE 0.021 0.002 PHE m 264 TYR 0.021 0.001 TYR A 72 ARG 0.002 0.000 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 fitting. rotamer outliers: 78 poor density : 162 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.6684 (p0) cc_final: 0.6432 (p0) REVERT: A 80 GLU cc_start: 0.6147 (mt-10) cc_final: 0.5790 (tt0) REVERT: C 152 ILE cc_start: 0.5020 (OUTLIER) cc_final: 0.4769 (tt) REVERT: D 163 TRP cc_start: 0.6492 (m100) cc_final: 0.6102 (m-10) REVERT: D 180 LYS cc_start: 0.6620 (OUTLIER) cc_final: 0.5927 (mttm) REVERT: e 121 ASN cc_start: 0.7453 (t0) cc_final: 0.7240 (t0) REVERT: f 111 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6568 (t80) REVERT: f 149 TYR cc_start: 0.4666 (OUTLIER) cc_final: 0.4219 (t80) outliers start: 78 outliers final: 51 residues processed: 223 average time/residue: 0.1757 time to fit residues: 59.6373 Evaluate side-chains 210 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 155 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 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 57 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 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 72 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10685 Z= 0.355 Angle : 0.667 7.924 14535 Z= 0.345 Chirality : 0.045 0.240 1704 Planarity : 0.004 0.048 1804 Dihedral : 5.890 58.282 1473 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 7.66 % Allowed : 26.67 % Favored : 65.67 % 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: -0.25 (0.23), residues: 1330 helix: 1.73 (0.30), residues: 272 sheet: -0.40 (0.23), residues: 474 loop : -0.79 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 36 HIS 0.003 0.001 HIS D 173 PHE 0.021 0.002 PHE A 99 TYR 0.021 0.002 TYR A 72 ARG 0.004 0.000 ARG g 102 *********************** 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 253 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 166 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 180 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6314 (mttm) REVERT: e 56 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: e 121 ASN cc_start: 0.7653 (t0) cc_final: 0.7327 (t0) REVERT: f 111 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6862 (t80) REVERT: f 149 TYR cc_start: 0.4767 (OUTLIER) cc_final: 0.4260 (t80) outliers start: 87 outliers final: 67 residues processed: 235 average time/residue: 0.1730 time to fit residues: 62.0643 Evaluate side-chains 224 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 153 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 94 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 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 89 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 204 CYS Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 39 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 42 THR Chi-restraints excluded: chain d residue 65 LEU Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain e residue 43 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 89 GLU Chi-restraints excluded: chain e residue 112 LEU Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain f residue 44 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 65 ASN Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 83 SER Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.0370 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 67 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10685 Z= 0.184 Angle : 0.585 10.158 14535 Z= 0.300 Chirality : 0.042 0.207 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.569 59.098 1473 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 5.63 % Allowed : 28.08 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.55 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1330 helix: 2.02 (0.30), residues: 272 sheet: -0.28 (0.23), residues: 473 loop : -0.65 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 163 HIS 0.003 0.001 HIS d 89 PHE 0.013 0.001 PHE A 211 TYR 0.021 0.001 TYR A 72 ARG 0.004 0.000 ARG m 253 *********************** 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 232 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 168 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 180 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6397 (mttt) REVERT: f 46 ILE cc_start: 0.8528 (mt) cc_final: 0.8221 (mt) REVERT: f 111 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6628 (t80) REVERT: f 149 TYR cc_start: 0.4430 (OUTLIER) cc_final: 0.4160 (t80) outliers start: 64 outliers final: 46 residues processed: 217 average time/residue: 0.1720 time to fit residues: 56.7676 Evaluate side-chains 205 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 94 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 33 THR Chi-restraints excluded: chain B residue 70 LEU 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 34 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 76 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 70 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain d residue 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 97 VAL Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10685 Z= 0.385 Angle : 0.692 10.107 14535 Z= 0.359 Chirality : 0.046 0.298 1704 Planarity : 0.005 0.050 1804 Dihedral : 5.812 57.390 1471 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 7.22 % Allowed : 27.20 % Favored : 65.58 % 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: -0.30 (0.22), residues: 1330 helix: 1.80 (0.30), residues: 272 sheet: -0.46 (0.23), residues: 467 loop : -0.86 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 36 HIS 0.005 0.001 HIS D 173 PHE 0.023 0.002 PHE A 99 TYR 0.024 0.002 TYR A 72 ARG 0.005 0.001 ARG g 102 *********************** 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 240 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 158 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: B 70 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7098 (mt) REVERT: D 180 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6406 (mttt) REVERT: e 56 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7018 (tp30) REVERT: f 46 ILE cc_start: 0.8568 (mt) cc_final: 0.8285 (mt) REVERT: f 111 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6880 (t80) REVERT: f 149 TYR cc_start: 0.4706 (OUTLIER) cc_final: 0.4183 (t80) outliers start: 82 outliers final: 63 residues processed: 223 average time/residue: 0.1727 time to fit residues: 58.9998 Evaluate side-chains 222 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 154 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 94 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 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 94 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 41 HIS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain b residue 51 LEU 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 112 LEU 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 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain m residue 266 LEU Chi-restraints excluded: chain n residue 250 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.0010 chunk 38 optimal weight: 0.4980 chunk 24 optimal weight: 0.0570 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN C 7 GLN C 38 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10685 Z= 0.204 Angle : 0.623 11.160 14535 Z= 0.318 Chirality : 0.043 0.235 1704 Planarity : 0.004 0.046 1804 Dihedral : 5.546 59.576 1471 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.72 % Allowed : 29.14 % Favored : 65.14 % 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: -0.13 (0.23), residues: 1330 helix: 2.01 (0.30), residues: 272 sheet: -0.42 (0.23), residues: 471 loop : -0.72 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 163 HIS 0.003 0.001 HIS d 89 PHE 0.037 0.002 PHE m 264 TYR 0.021 0.002 TYR A 72 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 fitting. rotamer outliers: 65 poor density : 162 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: B 70 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7041 (mt) REVERT: D 180 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6377 (mttt) REVERT: f 46 ILE cc_start: 0.8532 (mt) cc_final: 0.8223 (mt) REVERT: f 111 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6709 (t80) REVERT: f 149 TYR cc_start: 0.4230 (OUTLIER) cc_final: 0.4014 (t80) outliers start: 65 outliers final: 52 residues processed: 211 average time/residue: 0.1762 time to fit residues: 56.3595 Evaluate side-chains 215 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 159 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR 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 94 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 LEU 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 28 GLN 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 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 144 MET Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain 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 37 CYS 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 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 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 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 118 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10685 Z= 0.419 Angle : 0.725 11.045 14535 Z= 0.374 Chirality : 0.047 0.308 1704 Planarity : 0.005 0.055 1804 Dihedral : 5.927 56.765 1471 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.51 % Allowed : 28.17 % Favored : 65.32 % 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: -0.45 (0.22), residues: 1330 helix: 1.77 (0.30), residues: 272 sheet: -0.61 (0.23), residues: 473 loop : -0.95 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP D 163 HIS 0.004 0.001 HIS D 173 PHE 0.027 0.002 PHE A 99 TYR 0.024 0.002 TYR B 108 ARG 0.005 0.001 ARG g 102 *********************** 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 228 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 154 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: B 70 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7092 (mt) REVERT: D 180 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6388 (mttt) REVERT: e 56 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: f 46 ILE cc_start: 0.8566 (mt) cc_final: 0.8285 (mt) REVERT: f 111 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6883 (t80) REVERT: f 149 TYR cc_start: 0.4509 (OUTLIER) cc_final: 0.4171 (t80) outliers start: 74 outliers final: 60 residues processed: 214 average time/residue: 0.1733 time to fit residues: 56.2941 Evaluate side-chains 214 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 149 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 94 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 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 41 HIS 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 144 MET Chi-restraints excluded: chain D residue 160 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 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 e residue 43 THR Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 112 LEU 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 98 CYS Chi-restraints excluded: chain f residue 103 SER Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 114 LEU Chi-restraints excluded: chain f residue 149 TYR Chi-restraints excluded: chain g residue 45 THR Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 245 MET Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain 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 59 optimal weight: 0.0980 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 111 optimal weight: 0.3980 chunk 32 optimal weight: 0.0030 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3363 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= 0.197 Angle : 0.627 11.727 14535 Z= 0.320 Chirality : 0.043 0.269 1704 Planarity : 0.004 0.047 1804 Dihedral : 5.549 58.908 1471 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.02 % Allowed : 29.84 % Favored : 65.14 % 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: -0.15 (0.23), residues: 1330 helix: 2.04 (0.30), residues: 273 sheet: -0.44 (0.23), residues: 471 loop : -0.75 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 163 HIS 0.004 0.001 HIS d 89 PHE 0.019 0.001 PHE m 264 TYR 0.022 0.001 TYR A 72 ARG 0.003 0.000 ARG m 253 ********************** 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 218 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 161 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: D 180 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6309 (mttt) REVERT: e 56 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: f 46 ILE cc_start: 0.8519 (mt) cc_final: 0.8209 (mt) REVERT: f 111 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6624 (t80) REVERT: f 149 TYR cc_start: 0.4206 (OUTLIER) cc_final: 0.3993 (t80) outliers start: 57 outliers final: 45 residues processed: 207 average time/residue: 0.1818 time to fit residues: 56.7481 Evaluate side-chains 208 residues out of total 1222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 159 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 174 THR 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 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 182 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 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 a residue 34 LEU Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 41 ILE Chi-restraints excluded: chain 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 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 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 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 96 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4597 r_free = 0.4597 target = 0.205314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.171786 restraints weight = 13231.747| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 3.22 r_work: 0.3950 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10685 Z= 0.297 Angle : 0.673 10.940 14535 Z= 0.342 Chirality : 0.045 0.288 1704 Planarity : 0.004 0.048 1804 Dihedral : 5.648 57.000 1471 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.02 % Allowed : 30.02 % Favored : 64.96 % 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 (0.23), residues: 1330 helix: 2.00 (0.30), residues: 273 sheet: -0.52 (0.23), residues: 471 loop : -0.78 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 163 HIS 0.003 0.001 HIS d 89 PHE 0.025 0.002 PHE m 264 TYR 0.026 0.002 TYR D 80 ARG 0.003 0.000 ARG g 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3087.00 seconds wall clock time: 55 minutes 33.75 seconds (3333.75 seconds total)