Starting phenix.real_space_refine on Mon Dec 30 13:31:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqn_36576/12_2024/8jqn_36576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqn_36576/12_2024/8jqn_36576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqn_36576/12_2024/8jqn_36576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqn_36576/12_2024/8jqn_36576.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqn_36576/12_2024/8jqn_36576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqn_36576/12_2024/8jqn_36576.cif" } resolution = 2.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5334 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5610 2.51 5 N 1555 2.21 5 O 1700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8919 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} 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: "L" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 774 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "h" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "l" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "a" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2788 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 352, 2788 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2860 Chain: "A" Number of atoms: 2785 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 354, 2778 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 354, 2778 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 2848 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER a 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 58 " occ=0.50 residue: pdb=" N AVAL A 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 60 " occ=0.50 Time building chain proxies: 9.23, per 1000 atoms: 1.03 Number of scatterers: 8919 At special positions: 0 Unit cell: (124.95, 79.05, 163.2, 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 54 16.00 O 1700 8.00 N 1555 7.00 C 5610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.04 Simple disulfide: pdb=" SG CYS l 22 " - pdb=" SG CYS l 87 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 16.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.736A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.611A pdb=" N ASP L 81 " --> pdb=" O GLN L 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU L 82 " --> pdb=" O VAL L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.692A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 65 Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'h' and resid 101 through 105 removed outlier: 3.779A pdb=" N GLY h 105 " --> pdb=" O GLY h 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 82 removed outlier: 3.573A pdb=" N ASP l 81 " --> pdb=" O GLN l 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 82 removed outlier: 5.263A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 157 through 160 removed outlier: 4.478A pdb=" N PHE a 160 " --> pdb=" O ASP a 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 157 through 160' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.779A pdb=" N VAL a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.779A pdb=" N THR a 256 " --> pdb=" O HIS a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.577A pdb=" N ASN a 344 " --> pdb=" O PRO a 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.076A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.897A pdb=" N VAL A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.822A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.615A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.512A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.772A pdb=" N ALA L 83 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.772A pdb=" N ALA L 83 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.507A pdb=" N MET L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.607A pdb=" N TYR h 94 " --> pdb=" O THR h 112 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET h 34 " --> pdb=" O PHE h 50 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 9 through 12 removed outlier: 6.652A pdb=" N TRP l 34 " --> pdb=" O VAL l 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'l' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'l' and resid 18 through 23 removed outlier: 3.515A pdb=" N ALA l 18 " --> pdb=" O ILE l 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 2 through 7 removed outlier: 5.130A pdb=" N HIS A 1 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.790A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL a 89 " --> pdb=" O VAL a 135 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 153 through 155 Processing sheet with id=AB5, first strand: chain 'a' and resid 329 through 331 removed outlier: 4.474A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.454A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.515A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.325A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 285 through 287 296 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1480 1.31 - 1.44: 2628 1.44 - 1.57: 4972 1.57 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9156 Sorted by residual: bond pdb=" CA SER L 89 " pdb=" CB SER L 89 " ideal model delta sigma weight residual 1.534 1.436 0.098 1.34e-02 5.57e+03 5.40e+01 bond pdb=" C VAL a 167 " pdb=" O VAL a 167 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.11e-02 8.12e+03 2.30e+01 bond pdb=" CA SER L 93 " pdb=" CB SER L 93 " ideal model delta sigma weight residual 1.530 1.458 0.072 1.68e-02 3.54e+03 1.84e+01 bond pdb=" N ARG A 336 " pdb=" CA ARG A 336 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.75e+01 bond pdb=" C SER L 89 " pdb=" O SER L 89 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.08e-02 8.57e+03 1.52e+01 ... (remaining 9151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12120 1.94 - 3.88: 295 3.88 - 5.83: 26 5.83 - 7.77: 7 7.77 - 9.71: 2 Bond angle restraints: 12450 Sorted by residual: angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 114.12 104.50 9.62 1.39e+00 5.18e-01 4.79e+01 angle pdb=" C LYS A 206 " pdb=" CA LYS A 206 " pdb=" CB LYS A 206 " ideal model delta sigma weight residual 110.16 100.45 9.71 1.66e+00 3.63e-01 3.42e+01 angle pdb=" C HIS a 158 " pdb=" CA HIS a 158 " pdb=" CB HIS a 158 " ideal model delta sigma weight residual 111.50 117.81 -6.31 1.29e+00 6.01e-01 2.39e+01 angle pdb=" N THR a 165 " pdb=" CA THR a 165 " pdb=" C THR a 165 " ideal model delta sigma weight residual 114.64 108.42 6.22 1.52e+00 4.33e-01 1.67e+01 angle pdb=" N ASN L 95 " pdb=" CA ASN L 95 " pdb=" C ASN L 95 " ideal model delta sigma weight residual 114.31 109.19 5.12 1.29e+00 6.01e-01 1.57e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5011 17.53 - 35.06: 324 35.06 - 52.59: 59 52.59 - 70.12: 14 70.12 - 87.66: 4 Dihedral angle restraints: 5412 sinusoidal: 2116 harmonic: 3296 Sorted by residual: dihedral pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " pdb=" SG CYS a 312 " pdb=" CB CYS a 312 " ideal model delta sinusoidal sigma weight residual -86.00 -130.96 44.96 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" C HIS a 164 " pdb=" N HIS a 164 " pdb=" CA HIS a 164 " pdb=" CB HIS a 164 " ideal model delta harmonic sigma weight residual -122.60 -111.91 -10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C LYS A 206 " pdb=" N LYS A 206 " pdb=" CA LYS A 206 " pdb=" CB LYS A 206 " ideal model delta harmonic sigma weight residual -122.60 -112.01 -10.59 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1055 0.055 - 0.110: 217 0.110 - 0.166: 51 0.166 - 0.221: 6 0.221 - 0.276: 1 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA HIS a 164 " pdb=" N HIS a 164 " pdb=" C HIS a 164 " pdb=" CB HIS a 164 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LEU L 96 " pdb=" N LEU L 96 " pdb=" C LEU L 96 " pdb=" CB LEU L 96 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA GLN l 78 " pdb=" N GLN l 78 " pdb=" C GLN l 78 " pdb=" CB GLN l 78 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1327 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA l 77 " -0.022 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C ALA l 77 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA l 77 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN l 78 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE h 100 " 0.016 2.00e-02 2.50e+03 1.49e-02 3.90e+00 pdb=" CG PHE h 100 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE h 100 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE h 100 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE h 100 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE h 100 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE h 100 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR l 33 " -0.014 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR l 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR l 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR l 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR l 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR l 33 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR l 33 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR l 33 " -0.000 2.00e-02 2.50e+03 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1509 2.76 - 3.30: 7748 3.30 - 3.83: 13916 3.83 - 4.37: 17037 4.37 - 4.90: 30629 Nonbonded interactions: 70839 Sorted by model distance: nonbonded pdb=" OG SER A 297 " pdb=" O TYR A 331 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP A 197 " pdb=" NZ LYS A 221 " model vdw 2.239 3.120 nonbonded pdb=" OE2 GLU L 82 " pdb=" N VAL L 107 " model vdw 2.241 3.120 nonbonded pdb=" OD2 ASP a 197 " pdb=" NZ LYS a 221 " model vdw 2.273 3.120 nonbonded pdb=" OG SER a 297 " pdb=" O TYR a 331 " model vdw 2.273 3.040 ... (remaining 70834 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 1 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 57 or resid 59 or resid 61 through \ 257 or (resid 258 and (name N or name CA or name C or name O or name CB )) or re \ sid 259 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 309 or (resid 310 and (name N or name CA or name \ C or name O or name CB )) or resid 311 through 352)) selection = (chain 'a' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 25 or (resid 26 through 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 and (n \ ame N or name CA or name C or name O or name CB )) or resid 32 through 57 or res \ id 59 or resid 61 through 121 or (resid 122 and (name N or name CA or name C or \ name O or name CB )) or resid 123 through 124 or (resid 125 through 127 and (nam \ e N or name CA or name C or name O or name CB )) or resid 128 through 288 or (re \ sid 289 and (name N or name CA or name C or name O or name CB )) or resid 290 th \ rough 314 or (resid 315 and (name N or name CA or name C or name O or name CB )) \ or resid 316 through 325 or (resid 326 and (name N or name CA or name C or name \ O or name CB )) or resid 327 through 352)) } ncs_group { reference = (chain 'H' and (resid 2 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 86 or (resid 87 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 117)) selection = chain 'h' } ncs_group { reference = (chain 'L' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 108)) selection = (chain 'l' and (resid 4 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 108)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.200 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 : 0.007 0.098 9156 Z= 0.442 Angle : 0.712 9.712 12450 Z= 0.447 Chirality : 0.049 0.276 1330 Planarity : 0.004 0.045 1606 Dihedral : 12.256 87.655 3262 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Rotamer: Outliers : 1.37 % Allowed : 0.84 % Favored : 97.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.89 (0.25), residues: 1143 helix: 2.08 (0.59), residues: 73 sheet: -0.62 (0.28), residues: 369 loop : -0.84 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 168 HIS 0.009 0.001 HIS a 164 PHE 0.035 0.002 PHE h 100 TYR 0.031 0.002 TYR l 33 ARG 0.005 0.001 ARG a 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 VAL cc_start: 0.8306 (t) cc_final: 0.7992 (p) REVERT: H 43 LYS cc_start: 0.6206 (mppt) cc_final: 0.5854 (mtmt) REVERT: H 57 ASN cc_start: 0.8146 (m-40) cc_final: 0.7876 (m110) REVERT: H 71 SER cc_start: 0.8053 (t) cc_final: 0.7654 (p) REVERT: L 29 LYS cc_start: 0.6847 (mttt) cc_final: 0.6375 (mtmt) REVERT: L 62 SER cc_start: 0.7697 (t) cc_final: 0.7354 (m) REVERT: L 69 MET cc_start: 0.6794 (ttm) cc_final: 0.6536 (ttm) REVERT: L 84 ASP cc_start: 0.7431 (m-30) cc_final: 0.7102 (m-30) REVERT: h 78 THR cc_start: 0.6922 (m) cc_final: 0.6652 (t) REVERT: l 29 LYS cc_start: 0.5390 (mmmt) cc_final: 0.5105 (mttp) REVERT: l 60 ARG cc_start: 0.6761 (ptt180) cc_final: 0.6555 (ptt180) REVERT: l 82 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6286 (tp30) REVERT: a 10 LYS cc_start: 0.6736 (mttt) cc_final: 0.6329 (mttp) REVERT: a 11 LYS cc_start: 0.6850 (mtpt) cc_final: 0.5319 (tppt) REVERT: a 24 ASP cc_start: 0.7349 (p0) cc_final: 0.7061 (p0) REVERT: a 72 GLU cc_start: 0.6003 (tt0) cc_final: 0.5792 (tt0) REVERT: a 142 GLU cc_start: 0.6634 (tt0) cc_final: 0.6331 (mt-10) REVERT: a 156 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6224 (mt-10) REVERT: a 165 THR cc_start: 0.5960 (OUTLIER) cc_final: 0.5461 (m) REVERT: a 166 SER cc_start: 0.7125 (OUTLIER) cc_final: 0.6869 (p) REVERT: a 170 LYS cc_start: 0.7620 (ptmm) cc_final: 0.7049 (ptmm) REVERT: a 189 LYS cc_start: 0.7770 (tptm) cc_final: 0.7014 (tptp) REVERT: a 192 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6832 (mm-30) REVERT: a 261 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.6496 (mtp180) REVERT: a 264 MET cc_start: 0.7917 (mmt) cc_final: 0.7313 (mmt) REVERT: a 271 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7342 (mm-30) REVERT: a 279 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6897 (mt-10) REVERT: a 302 THR cc_start: 0.7665 (m) cc_final: 0.7051 (p) REVERT: A 10 LYS cc_start: 0.7677 (mptt) cc_final: 0.7313 (mmtt) REVERT: A 40 ARG cc_start: 0.6548 (mpp80) cc_final: 0.5863 (mtt90) REVERT: A 52 ASP cc_start: 0.6806 (t70) cc_final: 0.6556 (m-30) REVERT: A 109 ASN cc_start: 0.7143 (m-40) cc_final: 0.6847 (t0) REVERT: A 128 LYS cc_start: 0.6815 (tttp) cc_final: 0.6521 (ttmt) REVERT: A 130 ASN cc_start: 0.6839 (p0) cc_final: 0.6200 (m110) REVERT: A 138 ASP cc_start: 0.6764 (t0) cc_final: 0.6554 (m-30) REVERT: A 178 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 209 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7464 (m) REVERT: A 274 GLU cc_start: 0.7685 (tt0) cc_final: 0.7387 (tt0) REVERT: A 284 LYS cc_start: 0.7909 (tttp) cc_final: 0.7073 (tptp) outliers start: 12 outliers final: 1 residues processed: 218 average time/residue: 1.2570 time to fit residues: 291.7168 Evaluate side-chains 155 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 82 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 166 SER Chi-restraints excluded: chain A residue 209 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 41 GLN a 2 HIS a 82 ASN a 102 GLN a 131 ASN A 85 GLN A 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9156 Z= 0.215 Angle : 0.605 7.894 12450 Z= 0.329 Chirality : 0.045 0.148 1330 Planarity : 0.004 0.035 1606 Dihedral : 5.253 42.801 1265 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.89 % Allowed : 8.82 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.73 (0.25), residues: 1143 helix: 1.87 (0.59), residues: 77 sheet: -0.55 (0.27), residues: 380 loop : -0.68 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.006 0.001 HIS a 2 PHE 0.025 0.002 PHE h 100 TYR 0.026 0.002 TYR H 103 ARG 0.008 0.001 ARG a 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: H 11 VAL cc_start: 0.8260 (t) cc_final: 0.8050 (p) REVERT: H 43 LYS cc_start: 0.6140 (mppt) cc_final: 0.5712 (mtpt) REVERT: H 57 ASN cc_start: 0.8103 (m-40) cc_final: 0.7817 (m110) REVERT: H 71 SER cc_start: 0.8008 (t) cc_final: 0.7477 (p) REVERT: L 29 LYS cc_start: 0.6526 (mttt) cc_final: 0.6043 (mtpt) REVERT: L 62 SER cc_start: 0.7374 (t) cc_final: 0.6830 (p) REVERT: h 71 SER cc_start: 0.7837 (m) cc_final: 0.7432 (p) REVERT: h 78 THR cc_start: 0.7023 (m) cc_final: 0.6784 (t) REVERT: l 29 LYS cc_start: 0.5629 (mmmt) cc_final: 0.5118 (mttp) REVERT: a 10 LYS cc_start: 0.6992 (mttt) cc_final: 0.6563 (mttp) REVERT: a 40 ARG cc_start: 0.6698 (mtm110) cc_final: 0.6302 (mtm-85) REVERT: a 72 GLU cc_start: 0.6109 (tt0) cc_final: 0.5872 (tt0) REVERT: a 110 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6231 (pt0) REVERT: a 136 ASP cc_start: 0.7833 (p0) cc_final: 0.7318 (p0) REVERT: a 142 GLU cc_start: 0.6657 (tt0) cc_final: 0.6320 (mt-10) REVERT: a 166 SER cc_start: 0.7028 (OUTLIER) cc_final: 0.6783 (p) REVERT: a 170 LYS cc_start: 0.7545 (ptmm) cc_final: 0.6970 (ptmm) REVERT: a 189 LYS cc_start: 0.7202 (tptm) cc_final: 0.6559 (tptp) REVERT: a 192 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6753 (mm-30) REVERT: a 213 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7708 (tttt) REVERT: a 237 GLU cc_start: 0.7053 (pt0) cc_final: 0.6548 (pm20) REVERT: a 238 GLU cc_start: 0.7537 (tt0) cc_final: 0.7289 (mt-10) REVERT: a 261 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.6485 (mtp180) REVERT: a 264 MET cc_start: 0.7857 (mmt) cc_final: 0.7348 (mmt) REVERT: a 271 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7232 (mm-30) REVERT: a 302 THR cc_start: 0.7786 (m) cc_final: 0.7237 (p) REVERT: a 317 THR cc_start: 0.7716 (m) cc_final: 0.7444 (p) REVERT: a 338 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7328 (ttp80) REVERT: A 10 LYS cc_start: 0.7962 (mptt) cc_final: 0.7595 (mmmt) REVERT: A 12 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6117 (mm-30) REVERT: A 40 ARG cc_start: 0.6588 (mpp80) cc_final: 0.5955 (mtt90) REVERT: A 94 LYS cc_start: 0.7577 (tttm) cc_final: 0.7227 (ptmm) REVERT: A 109 ASN cc_start: 0.7087 (m-40) cc_final: 0.6807 (t0) REVERT: A 128 LYS cc_start: 0.6763 (tttp) cc_final: 0.6469 (ttmt) REVERT: A 130 ASN cc_start: 0.6856 (p0) cc_final: 0.6202 (m110) REVERT: A 138 ASP cc_start: 0.6776 (t0) cc_final: 0.6532 (m-30) REVERT: A 178 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6659 (mt-10) REVERT: A 284 LYS cc_start: 0.7822 (tttp) cc_final: 0.7008 (tptp) outliers start: 17 outliers final: 9 residues processed: 158 average time/residue: 1.3662 time to fit residues: 229.3557 Evaluate side-chains 153 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 166 SER Chi-restraints excluded: chain a residue 213 LYS Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 41 GLN a 2 HIS a 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9156 Z= 0.240 Angle : 0.616 10.917 12450 Z= 0.330 Chirality : 0.046 0.207 1330 Planarity : 0.005 0.034 1606 Dihedral : 4.962 37.579 1260 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.84 % Allowed : 10.08 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.63 (0.25), residues: 1143 helix: 1.66 (0.57), residues: 77 sheet: -0.36 (0.27), residues: 374 loop : -0.66 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.006 0.001 HIS H 35 PHE 0.027 0.002 PHE h 100 TYR 0.025 0.002 TYR H 103 ARG 0.007 0.001 ARG a 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6155 (mppt) cc_final: 0.5679 (mtpt) REVERT: H 57 ASN cc_start: 0.8102 (m-40) cc_final: 0.7807 (m110) REVERT: H 71 SER cc_start: 0.7887 (t) cc_final: 0.7371 (p) REVERT: L 23 SER cc_start: 0.8034 (p) cc_final: 0.7383 (t) REVERT: L 62 SER cc_start: 0.7240 (t) cc_final: 0.6690 (p) REVERT: h 71 SER cc_start: 0.7854 (m) cc_final: 0.7430 (p) REVERT: l 29 LYS cc_start: 0.5907 (mmmt) cc_final: 0.5377 (mttp) REVERT: l 69 MET cc_start: 0.7328 (mmt) cc_final: 0.7034 (mmt) REVERT: l 84 ASP cc_start: 0.7223 (m-30) cc_final: 0.6893 (m-30) REVERT: a 10 LYS cc_start: 0.7113 (mttt) cc_final: 0.6628 (mtmp) REVERT: a 40 ARG cc_start: 0.6707 (mtm110) cc_final: 0.6462 (mtm-85) REVERT: a 72 GLU cc_start: 0.6098 (tt0) cc_final: 0.5875 (tt0) REVERT: a 74 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6495 (mt-10) REVERT: a 142 GLU cc_start: 0.6640 (tt0) cc_final: 0.6275 (mt-10) REVERT: a 170 LYS cc_start: 0.7460 (ptmm) cc_final: 0.6845 (ptpp) REVERT: a 189 LYS cc_start: 0.7141 (tptm) cc_final: 0.6504 (tptp) REVERT: a 192 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6689 (mm-30) REVERT: a 237 GLU cc_start: 0.7036 (pt0) cc_final: 0.6521 (pm20) REVERT: a 261 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6431 (mtp180) REVERT: a 271 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7206 (mm-30) REVERT: a 302 THR cc_start: 0.7655 (m) cc_final: 0.7154 (p) REVERT: a 317 THR cc_start: 0.7753 (m) cc_final: 0.7533 (p) REVERT: a 326 LYS cc_start: 0.7802 (tttt) cc_final: 0.7587 (tttp) REVERT: a 338 ARG cc_start: 0.7567 (ttp-170) cc_final: 0.7328 (ttp80) REVERT: A 10 LYS cc_start: 0.7991 (mptt) cc_final: 0.7598 (mmmt) REVERT: A 12 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6040 (mm-30) REVERT: A 40 ARG cc_start: 0.6606 (mpp80) cc_final: 0.5924 (mtt90) REVERT: A 109 ASN cc_start: 0.7066 (m-40) cc_final: 0.6789 (t0) REVERT: A 128 LYS cc_start: 0.6763 (tttp) cc_final: 0.6533 (ttmt) REVERT: A 130 ASN cc_start: 0.6856 (p0) cc_final: 0.6204 (m110) REVERT: A 138 ASP cc_start: 0.6859 (t0) cc_final: 0.6555 (m-30) REVERT: A 272 GLU cc_start: 0.7750 (tt0) cc_final: 0.7359 (tt0) REVERT: A 284 LYS cc_start: 0.7721 (tttp) cc_final: 0.6912 (tptp) REVERT: A 309 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6870 (pm20) outliers start: 26 outliers final: 12 residues processed: 159 average time/residue: 1.3528 time to fit residues: 228.6051 Evaluate side-chains 145 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 309 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 41 GLN ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9156 Z= 0.185 Angle : 0.566 11.200 12450 Z= 0.304 Chirality : 0.044 0.208 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.722 34.970 1259 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.63 % Allowed : 11.13 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.55 (0.25), residues: 1143 helix: 1.55 (0.57), residues: 77 sheet: -0.30 (0.27), residues: 374 loop : -0.58 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.005 0.001 HIS h 35 PHE 0.017 0.002 PHE h 100 TYR 0.024 0.001 TYR H 103 ARG 0.006 0.000 ARG a 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6130 (mppt) cc_final: 0.5702 (mtpt) REVERT: H 57 ASN cc_start: 0.8143 (m-40) cc_final: 0.7823 (m110) REVERT: H 71 SER cc_start: 0.7863 (t) cc_final: 0.7338 (p) REVERT: L 49 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7916 (mt-10) REVERT: L 62 SER cc_start: 0.7229 (t) cc_final: 0.6942 (m) REVERT: h 71 SER cc_start: 0.7870 (m) cc_final: 0.7445 (p) REVERT: l 29 LYS cc_start: 0.5877 (mmmt) cc_final: 0.5354 (mttp) REVERT: l 69 MET cc_start: 0.7268 (mmt) cc_final: 0.7005 (mmt) REVERT: a 10 LYS cc_start: 0.7060 (mttt) cc_final: 0.6612 (mtmp) REVERT: a 40 ARG cc_start: 0.6683 (mtm110) cc_final: 0.6311 (mtm-85) REVERT: a 72 GLU cc_start: 0.6101 (tt0) cc_final: 0.5857 (tt0) REVERT: a 110 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6319 (pt0) REVERT: a 139 THR cc_start: 0.7775 (p) cc_final: 0.7339 (p) REVERT: a 142 GLU cc_start: 0.6615 (tt0) cc_final: 0.6262 (mt-10) REVERT: a 170 LYS cc_start: 0.7504 (ptmm) cc_final: 0.6878 (ptpp) REVERT: a 189 LYS cc_start: 0.7079 (tptm) cc_final: 0.6441 (tptp) REVERT: a 192 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6730 (mm-30) REVERT: a 237 GLU cc_start: 0.7086 (pt0) cc_final: 0.6546 (pm20) REVERT: a 261 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6423 (mtp180) REVERT: a 271 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7207 (mm-30) REVERT: a 302 THR cc_start: 0.7580 (m) cc_final: 0.7085 (p) REVERT: a 317 THR cc_start: 0.7738 (m) cc_final: 0.7526 (p) REVERT: a 326 LYS cc_start: 0.7821 (tttt) cc_final: 0.7620 (tttp) REVERT: a 338 ARG cc_start: 0.7536 (ttp-170) cc_final: 0.7288 (ttp80) REVERT: A 10 LYS cc_start: 0.7980 (mptt) cc_final: 0.7590 (mmmt) REVERT: A 12 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6034 (mm-30) REVERT: A 40 ARG cc_start: 0.6543 (mpp80) cc_final: 0.5833 (mtt90) REVERT: A 109 ASN cc_start: 0.7084 (m-40) cc_final: 0.6816 (t0) REVERT: A 128 LYS cc_start: 0.6807 (tttp) cc_final: 0.6520 (ttmt) REVERT: A 130 ASN cc_start: 0.6862 (p0) cc_final: 0.6194 (m110) REVERT: A 138 ASP cc_start: 0.6868 (t0) cc_final: 0.6540 (m-30) REVERT: A 238 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7127 (mt-10) REVERT: A 284 LYS cc_start: 0.7724 (tttp) cc_final: 0.6910 (tptp) REVERT: A 309 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6855 (pm20) outliers start: 24 outliers final: 12 residues processed: 149 average time/residue: 1.3691 time to fit residues: 217.0339 Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 309 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 0.0000 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 9156 Z= 0.471 Angle : 0.751 13.008 12450 Z= 0.402 Chirality : 0.052 0.265 1330 Planarity : 0.006 0.044 1606 Dihedral : 5.389 35.542 1259 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.15 % Allowed : 11.97 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.73 (0.25), residues: 1143 helix: 1.19 (0.57), residues: 77 sheet: -0.27 (0.27), residues: 374 loop : -0.79 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 168 HIS 0.008 0.002 HIS H 35 PHE 0.035 0.003 PHE h 100 TYR 0.029 0.003 TYR H 103 ARG 0.011 0.001 ARG a 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6317 (mppt) cc_final: 0.5843 (mtpt) REVERT: H 57 ASN cc_start: 0.8020 (m-40) cc_final: 0.7732 (m110) REVERT: H 71 SER cc_start: 0.7810 (t) cc_final: 0.7265 (p) REVERT: L 62 SER cc_start: 0.7298 (t) cc_final: 0.6781 (p) REVERT: L 84 ASP cc_start: 0.7215 (m-30) cc_final: 0.6835 (m-30) REVERT: h 71 SER cc_start: 0.7820 (m) cc_final: 0.7434 (p) REVERT: h 104 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: l 29 LYS cc_start: 0.5962 (mmmt) cc_final: 0.5437 (mttp) REVERT: l 69 MET cc_start: 0.7288 (mmt) cc_final: 0.7054 (mmt) REVERT: a 10 LYS cc_start: 0.7119 (mttt) cc_final: 0.6754 (mtmp) REVERT: a 40 ARG cc_start: 0.6639 (mtm110) cc_final: 0.6284 (mtt180) REVERT: a 72 GLU cc_start: 0.6125 (tt0) cc_final: 0.5922 (tt0) REVERT: a 74 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: a 110 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6415 (pt0) REVERT: a 142 GLU cc_start: 0.6674 (tt0) cc_final: 0.6301 (mt-10) REVERT: a 170 LYS cc_start: 0.7577 (ptmm) cc_final: 0.7017 (ptmm) REVERT: a 189 LYS cc_start: 0.7223 (tptm) cc_final: 0.6570 (tptp) REVERT: a 192 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6692 (mm-30) REVERT: a 237 GLU cc_start: 0.6968 (pt0) cc_final: 0.6489 (pm20) REVERT: a 261 ARG cc_start: 0.7350 (mmm-85) cc_final: 0.6490 (mtp180) REVERT: a 271 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7191 (mm-30) REVERT: a 302 THR cc_start: 0.7703 (m) cc_final: 0.7228 (p) REVERT: a 326 LYS cc_start: 0.7806 (tttt) cc_final: 0.7603 (tttp) REVERT: a 338 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7324 (ttp80) REVERT: A 10 LYS cc_start: 0.7933 (mptt) cc_final: 0.7553 (mtmp) REVERT: A 12 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6178 (mm-30) REVERT: A 40 ARG cc_start: 0.6661 (mpp80) cc_final: 0.6098 (mtt90) REVERT: A 109 ASN cc_start: 0.7120 (m-40) cc_final: 0.6817 (t0) REVERT: A 128 LYS cc_start: 0.6856 (tttp) cc_final: 0.6597 (tttt) REVERT: A 130 ASN cc_start: 0.7028 (p0) cc_final: 0.6211 (m110) REVERT: A 138 ASP cc_start: 0.7019 (t0) cc_final: 0.6630 (m-30) REVERT: A 238 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7166 (mt-10) REVERT: A 284 LYS cc_start: 0.7726 (tttp) cc_final: 0.6894 (tptp) outliers start: 29 outliers final: 19 residues processed: 151 average time/residue: 1.4011 time to fit residues: 224.3970 Evaluate side-chains 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 104 GLU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 50 ASP Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 25 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.0170 chunk 104 optimal weight: 1.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9156 Z= 0.187 Angle : 0.571 12.145 12450 Z= 0.308 Chirality : 0.044 0.209 1330 Planarity : 0.004 0.035 1606 Dihedral : 4.879 34.577 1259 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.21 % Allowed : 13.55 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.57 (0.25), residues: 1143 helix: 1.48 (0.57), residues: 77 sheet: -0.14 (0.27), residues: 372 loop : -0.70 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.005 0.001 HIS h 35 PHE 0.012 0.001 PHE a 277 TYR 0.022 0.001 TYR H 103 ARG 0.005 0.000 ARG a 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6199 (mppt) cc_final: 0.5742 (mtpt) REVERT: H 57 ASN cc_start: 0.8108 (m-40) cc_final: 0.7803 (m110) REVERT: H 71 SER cc_start: 0.7814 (t) cc_final: 0.7273 (p) REVERT: H 113 LEU cc_start: 0.7891 (tp) cc_final: 0.7595 (tm) REVERT: L 62 SER cc_start: 0.7164 (t) cc_final: 0.6704 (m) REVERT: h 71 SER cc_start: 0.7825 (m) cc_final: 0.7431 (p) REVERT: l 29 LYS cc_start: 0.5907 (mmmt) cc_final: 0.5448 (mttp) REVERT: l 69 MET cc_start: 0.7354 (mmt) cc_final: 0.7096 (mmt) REVERT: a 10 LYS cc_start: 0.7112 (mttt) cc_final: 0.6725 (mtmp) REVERT: a 12 GLU cc_start: 0.7090 (pt0) cc_final: 0.6829 (pt0) REVERT: a 40 ARG cc_start: 0.6626 (mtm110) cc_final: 0.6307 (mtt180) REVERT: a 72 GLU cc_start: 0.6182 (tt0) cc_final: 0.5947 (tt0) REVERT: a 74 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: a 110 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6315 (pt0) REVERT: a 142 GLU cc_start: 0.6604 (tt0) cc_final: 0.6272 (mp0) REVERT: a 170 LYS cc_start: 0.7567 (ptmm) cc_final: 0.6889 (ptpp) REVERT: a 189 LYS cc_start: 0.7127 (tptm) cc_final: 0.6483 (tptp) REVERT: a 237 GLU cc_start: 0.7071 (pt0) cc_final: 0.6602 (pm20) REVERT: a 261 ARG cc_start: 0.7298 (mmm-85) cc_final: 0.6428 (mtp180) REVERT: a 271 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7181 (mm-30) REVERT: a 302 THR cc_start: 0.7562 (m) cc_final: 0.7076 (p) REVERT: a 338 ARG cc_start: 0.7483 (ttp-170) cc_final: 0.7235 (ttp80) REVERT: A 10 LYS cc_start: 0.7896 (mptt) cc_final: 0.7505 (mtmp) REVERT: A 12 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6263 (mm-30) REVERT: A 40 ARG cc_start: 0.6424 (mpp80) cc_final: 0.5825 (mtt90) REVERT: A 109 ASN cc_start: 0.7138 (m-40) cc_final: 0.6869 (t0) REVERT: A 128 LYS cc_start: 0.6846 (tttp) cc_final: 0.6594 (tttt) REVERT: A 130 ASN cc_start: 0.6999 (p0) cc_final: 0.6173 (m110) REVERT: A 138 ASP cc_start: 0.7021 (t0) cc_final: 0.6649 (m-30) REVERT: A 284 LYS cc_start: 0.7701 (tttp) cc_final: 0.6883 (tptp) REVERT: A 309 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6798 (pm20) outliers start: 20 outliers final: 13 residues processed: 152 average time/residue: 1.3648 time to fit residues: 220.4293 Evaluate side-chains 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 309 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 101 ASN h 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9156 Z= 0.173 Angle : 0.552 13.116 12450 Z= 0.296 Chirality : 0.043 0.202 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.641 32.814 1259 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.42 % Allowed : 13.66 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.44 (0.25), residues: 1143 helix: 1.45 (0.57), residues: 77 sheet: -0.08 (0.28), residues: 372 loop : -0.57 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.005 0.001 HIS h 35 PHE 0.011 0.001 PHE a 277 TYR 0.022 0.001 TYR H 103 ARG 0.007 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6251 (mppt) cc_final: 0.5752 (mtpt) REVERT: H 57 ASN cc_start: 0.8099 (m-40) cc_final: 0.7793 (m110) REVERT: H 71 SER cc_start: 0.7828 (t) cc_final: 0.7146 (p) REVERT: H 113 LEU cc_start: 0.7872 (tp) cc_final: 0.7584 (tm) REVERT: L 49 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7954 (mt-10) REVERT: L 62 SER cc_start: 0.7190 (t) cc_final: 0.6736 (m) REVERT: h 71 SER cc_start: 0.7821 (m) cc_final: 0.7396 (p) REVERT: l 29 LYS cc_start: 0.5995 (mmmt) cc_final: 0.5415 (mttp) REVERT: l 69 MET cc_start: 0.7358 (mmt) cc_final: 0.7089 (mmt) REVERT: a 10 LYS cc_start: 0.7107 (mttt) cc_final: 0.6562 (mtmp) REVERT: a 12 GLU cc_start: 0.7058 (pt0) cc_final: 0.6816 (pt0) REVERT: a 40 ARG cc_start: 0.6675 (mtm110) cc_final: 0.6383 (mtt180) REVERT: a 72 GLU cc_start: 0.6204 (tt0) cc_final: 0.5967 (tt0) REVERT: a 74 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6538 (mt-10) REVERT: a 110 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6308 (pt0) REVERT: a 139 THR cc_start: 0.7778 (p) cc_final: 0.7362 (p) REVERT: a 142 GLU cc_start: 0.6572 (tt0) cc_final: 0.6226 (mp0) REVERT: a 170 LYS cc_start: 0.7524 (ptmm) cc_final: 0.6957 (ptmm) REVERT: a 189 LYS cc_start: 0.7054 (tptm) cc_final: 0.6413 (tptp) REVERT: a 237 GLU cc_start: 0.7079 (pt0) cc_final: 0.6612 (pm20) REVERT: a 261 ARG cc_start: 0.7289 (mmm-85) cc_final: 0.6410 (mtp180) REVERT: a 302 THR cc_start: 0.7518 (m) cc_final: 0.7023 (p) REVERT: a 338 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.7277 (ttp80) REVERT: A 10 LYS cc_start: 0.7844 (mptt) cc_final: 0.7428 (mtmp) REVERT: A 12 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6296 (mm-30) REVERT: A 40 ARG cc_start: 0.6366 (mpp80) cc_final: 0.5765 (mtt90) REVERT: A 109 ASN cc_start: 0.7204 (m-40) cc_final: 0.6940 (t0) REVERT: A 128 LYS cc_start: 0.6828 (tttp) cc_final: 0.6585 (tttt) REVERT: A 130 ASN cc_start: 0.6873 (p0) cc_final: 0.6185 (m110) REVERT: A 138 ASP cc_start: 0.6970 (t0) cc_final: 0.6596 (m-30) REVERT: A 237 GLU cc_start: 0.6111 (pm20) cc_final: 0.5478 (mp0) REVERT: A 271 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7165 (mm-30) REVERT: A 284 LYS cc_start: 0.7702 (tttp) cc_final: 0.6885 (tptp) outliers start: 22 outliers final: 13 residues processed: 153 average time/residue: 1.3510 time to fit residues: 220.0285 Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9156 Z= 0.187 Angle : 0.558 12.660 12450 Z= 0.299 Chirality : 0.044 0.207 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.669 34.835 1259 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.00 % Allowed : 14.08 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.38 (0.25), residues: 1143 helix: 1.53 (0.57), residues: 77 sheet: -0.04 (0.28), residues: 372 loop : -0.54 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.004 0.001 HIS A 195 PHE 0.012 0.001 PHE a 277 TYR 0.022 0.001 TYR H 103 ARG 0.006 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6309 (mppt) cc_final: 0.5799 (mtpt) REVERT: H 57 ASN cc_start: 0.8107 (m-40) cc_final: 0.7806 (m110) REVERT: H 71 SER cc_start: 0.7832 (t) cc_final: 0.7149 (p) REVERT: H 113 LEU cc_start: 0.7866 (tp) cc_final: 0.7580 (tm) REVERT: L 49 GLU cc_start: 0.8215 (mt-10) cc_final: 0.8011 (mt-10) REVERT: L 62 SER cc_start: 0.7193 (t) cc_final: 0.6743 (m) REVERT: h 71 SER cc_start: 0.7825 (m) cc_final: 0.7400 (p) REVERT: l 29 LYS cc_start: 0.5981 (mmmt) cc_final: 0.5428 (mttm) REVERT: l 69 MET cc_start: 0.7294 (mmt) cc_final: 0.7042 (mmt) REVERT: a 10 LYS cc_start: 0.7230 (mttt) cc_final: 0.6726 (mtmp) REVERT: a 12 GLU cc_start: 0.7136 (pt0) cc_final: 0.6874 (pt0) REVERT: a 40 ARG cc_start: 0.6693 (mtm110) cc_final: 0.6385 (mtt180) REVERT: a 51 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5408 (mp0) REVERT: a 72 GLU cc_start: 0.6182 (tt0) cc_final: 0.5946 (tt0) REVERT: a 74 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6528 (mt-10) REVERT: a 110 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6300 (pt0) REVERT: a 139 THR cc_start: 0.7783 (p) cc_final: 0.7350 (p) REVERT: a 142 GLU cc_start: 0.6572 (tt0) cc_final: 0.6276 (mp0) REVERT: a 170 LYS cc_start: 0.7556 (ptmm) cc_final: 0.6888 (ptpp) REVERT: a 189 LYS cc_start: 0.6989 (tptm) cc_final: 0.6341 (tptp) REVERT: a 237 GLU cc_start: 0.7084 (pt0) cc_final: 0.6610 (pm20) REVERT: a 261 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.6463 (mtp180) REVERT: a 302 THR cc_start: 0.7532 (m) cc_final: 0.7043 (p) REVERT: a 338 ARG cc_start: 0.7523 (ttp-170) cc_final: 0.7271 (ttp80) REVERT: A 10 LYS cc_start: 0.7820 (mptt) cc_final: 0.7428 (mtmp) REVERT: A 12 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6296 (mm-30) REVERT: A 40 ARG cc_start: 0.6387 (mpp80) cc_final: 0.5771 (mtt90) REVERT: A 109 ASN cc_start: 0.7239 (m-40) cc_final: 0.6983 (t0) REVERT: A 128 LYS cc_start: 0.6826 (tttp) cc_final: 0.6583 (tttt) REVERT: A 130 ASN cc_start: 0.6875 (p0) cc_final: 0.6188 (m110) REVERT: A 138 ASP cc_start: 0.7012 (t0) cc_final: 0.6575 (m-30) REVERT: A 237 GLU cc_start: 0.6002 (pm20) cc_final: 0.5470 (mp0) REVERT: A 271 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 284 LYS cc_start: 0.7709 (tttp) cc_final: 0.6888 (tptp) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 1.3916 time to fit residues: 221.9611 Evaluate side-chains 149 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9156 Z= 0.143 Angle : 0.521 13.581 12450 Z= 0.279 Chirality : 0.042 0.197 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.386 30.913 1259 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.00 % Allowed : 14.08 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.28 (0.26), residues: 1143 helix: 1.61 (0.58), residues: 77 sheet: -0.03 (0.28), residues: 373 loop : -0.43 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 150 HIS 0.004 0.001 HIS a 2 PHE 0.010 0.001 PHE a 277 TYR 0.022 0.001 TYR H 103 ARG 0.007 0.000 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6290 (mppt) cc_final: 0.5758 (mtmt) REVERT: H 57 ASN cc_start: 0.8103 (m-40) cc_final: 0.7789 (m110) REVERT: H 71 SER cc_start: 0.7844 (t) cc_final: 0.7186 (p) REVERT: H 113 LEU cc_start: 0.7846 (tp) cc_final: 0.7550 (tm) REVERT: L 62 SER cc_start: 0.7124 (t) cc_final: 0.6686 (m) REVERT: h 71 SER cc_start: 0.7799 (m) cc_final: 0.7382 (p) REVERT: l 69 MET cc_start: 0.7363 (mmt) cc_final: 0.7109 (mmt) REVERT: a 10 LYS cc_start: 0.7227 (mttt) cc_final: 0.6770 (mtmp) REVERT: a 72 GLU cc_start: 0.6178 (tt0) cc_final: 0.5947 (tt0) REVERT: a 110 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6370 (pt0) REVERT: a 139 THR cc_start: 0.7844 (p) cc_final: 0.7447 (p) REVERT: a 142 GLU cc_start: 0.6575 (tt0) cc_final: 0.6278 (mp0) REVERT: a 156 GLU cc_start: 0.6397 (mt-10) cc_final: 0.6173 (mt-10) REVERT: a 170 LYS cc_start: 0.7530 (ptmm) cc_final: 0.6889 (ptpp) REVERT: a 186 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7419 (m) REVERT: a 189 LYS cc_start: 0.6961 (tptm) cc_final: 0.6310 (tptp) REVERT: a 237 GLU cc_start: 0.7070 (pt0) cc_final: 0.6587 (pm20) REVERT: a 261 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.6421 (mtp180) REVERT: a 302 THR cc_start: 0.7536 (m) cc_final: 0.6993 (p) REVERT: a 338 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7279 (ttp80) REVERT: A 10 LYS cc_start: 0.7815 (mptt) cc_final: 0.7428 (mtmp) REVERT: A 12 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6307 (mm-30) REVERT: A 40 ARG cc_start: 0.6295 (mpp80) cc_final: 0.5695 (mtt90) REVERT: A 67 MET cc_start: 0.7228 (tmm) cc_final: 0.7027 (ttp) REVERT: A 109 ASN cc_start: 0.7222 (m-40) cc_final: 0.6990 (t0) REVERT: A 128 LYS cc_start: 0.6855 (tttp) cc_final: 0.6548 (ttmt) REVERT: A 130 ASN cc_start: 0.6858 (p0) cc_final: 0.6110 (m110) REVERT: A 138 ASP cc_start: 0.7009 (t0) cc_final: 0.6579 (m-30) REVERT: A 237 GLU cc_start: 0.5964 (pm20) cc_final: 0.5488 (mp0) REVERT: A 271 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 284 LYS cc_start: 0.7703 (tttp) cc_final: 0.6866 (tptp) outliers start: 18 outliers final: 11 residues processed: 154 average time/residue: 1.3948 time to fit residues: 229.2906 Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9156 Z= 0.269 Angle : 0.612 13.850 12450 Z= 0.327 Chirality : 0.046 0.223 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.889 38.058 1259 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.68 % Allowed : 14.60 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.36 (0.25), residues: 1143 helix: 1.54 (0.58), residues: 77 sheet: -0.01 (0.28), residues: 372 loop : -0.54 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 168 HIS 0.005 0.001 HIS A 195 PHE 0.016 0.002 PHE h 100 TYR 0.024 0.002 TYR H 103 ARG 0.006 0.001 ARG L 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.6379 (mppt) cc_final: 0.5885 (mtpt) REVERT: H 57 ASN cc_start: 0.8104 (m-40) cc_final: 0.7801 (m110) REVERT: H 71 SER cc_start: 0.7833 (t) cc_final: 0.7295 (p) REVERT: H 113 LEU cc_start: 0.7879 (tp) cc_final: 0.7591 (tm) REVERT: L 29 LYS cc_start: 0.6798 (mptt) cc_final: 0.6524 (mttm) REVERT: L 62 SER cc_start: 0.7254 (t) cc_final: 0.6793 (m) REVERT: L 84 ASP cc_start: 0.7296 (m-30) cc_final: 0.7061 (m-30) REVERT: h 71 SER cc_start: 0.7862 (m) cc_final: 0.7416 (p) REVERT: a 10 LYS cc_start: 0.7253 (mttt) cc_final: 0.6814 (mtmp) REVERT: a 40 ARG cc_start: 0.6708 (mtm180) cc_final: 0.6468 (mtt180) REVERT: a 72 GLU cc_start: 0.6216 (tt0) cc_final: 0.5981 (tt0) REVERT: a 110 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6252 (pt0) REVERT: a 142 GLU cc_start: 0.6554 (tt0) cc_final: 0.6273 (mp0) REVERT: a 156 GLU cc_start: 0.6412 (mt-10) cc_final: 0.6142 (mt-10) REVERT: a 170 LYS cc_start: 0.7676 (ptmm) cc_final: 0.6960 (ptpp) REVERT: a 189 LYS cc_start: 0.7040 (tptm) cc_final: 0.6388 (tptp) REVERT: a 237 GLU cc_start: 0.7061 (pt0) cc_final: 0.6602 (pm20) REVERT: a 261 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.6451 (mtp180) REVERT: a 302 THR cc_start: 0.7558 (m) cc_final: 0.7087 (p) REVERT: a 338 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.7239 (ttp80) REVERT: A 10 LYS cc_start: 0.7864 (mptt) cc_final: 0.7482 (mtmp) REVERT: A 12 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6270 (mm-30) REVERT: A 40 ARG cc_start: 0.6501 (mpp80) cc_final: 0.5899 (mtt90) REVERT: A 109 ASN cc_start: 0.7168 (m-40) cc_final: 0.6956 (t0) REVERT: A 128 LYS cc_start: 0.6819 (tttp) cc_final: 0.6575 (tttt) REVERT: A 130 ASN cc_start: 0.6870 (p0) cc_final: 0.6184 (m110) REVERT: A 138 ASP cc_start: 0.7053 (t0) cc_final: 0.6596 (m-30) REVERT: A 237 GLU cc_start: 0.6061 (pm20) cc_final: 0.5536 (mp0) REVERT: A 238 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6979 (mt-10) REVERT: A 271 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 284 LYS cc_start: 0.7689 (tttp) cc_final: 0.6870 (tptp) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 1.3570 time to fit residues: 206.5180 Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.0670 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 0.0370 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104372 restraints weight = 25686.100| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.26 r_work: 0.2898 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 9156 Z= 0.139 Angle : 0.515 13.215 12450 Z= 0.276 Chirality : 0.042 0.188 1330 Planarity : 0.004 0.035 1606 Dihedral : 4.379 30.018 1259 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.37 % Allowed : 15.13 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % 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: -0.20 (0.26), residues: 1143 helix: 1.62 (0.58), residues: 77 sheet: 0.02 (0.28), residues: 372 loop : -0.38 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 210 HIS 0.003 0.001 HIS a 2 PHE 0.009 0.001 PHE a 277 TYR 0.023 0.001 TYR H 103 ARG 0.007 0.000 ARG L 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4144.30 seconds wall clock time: 75 minutes 29.96 seconds (4529.96 seconds total)