Starting phenix.real_space_refine on Sat Feb 17 06:31:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wel_21651/02_2024/6wel_21651_neut_updated.pdb" } resolution = 2.5 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= 0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 S 96 5.16 5 Na 1 4.78 5 C 11640 2.51 5 N 2864 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B GLU 615": "OE1" <-> "OE2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C GLU 615": "OE1" <-> "OE2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 421": "NH1" <-> "NH2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "D ARG 614": "NH1" <-> "NH2" Residue "D GLU 615": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17725 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4235 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "B" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4235 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "C" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4235 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "D" Number of atoms: 4235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4235 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 15, 'TRANS': 497} Chain breaks: 1 Chain: "A" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 197 Unusual residues: {' NA': 1, 'CPL': 7, 'PX2': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 5, 'CPL:plan-1': 5} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Unusual residues: {'CPL': 7, 'PX2': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 5, 'CPL:plan-1': 5} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Unusual residues: {'CPL': 7, 'PX2': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 5, 'CPL:plan-1': 5} Unresolved non-hydrogen planarities: 77 Chain: "D" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Unusual residues: {'CPL': 7, 'PX2': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 5, 'CPL:plan-2': 5, 'CPL:plan-1': 5} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 9.33, per 1000 atoms: 0.53 Number of scatterers: 17725 At special positions: 0 Unit cell: (130.38, 130.38, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 16 15.00 Na 1 11.00 O 3108 8.00 N 2864 7.00 C 11640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 2.9 seconds 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 12 sheets defined 55.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 119 through 144 removed outlier: 4.730A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 194 through 223 removed outlier: 6.599A pdb=" N HIS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.788A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.986A pdb=" N LEU A 264 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 4.266A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 304 through 334 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 416 Processing helix chain 'A' and resid 419 through 437 Processing helix chain 'A' and resid 442 through 456 Processing helix chain 'A' and resid 465 through 470 removed outlier: 4.117A pdb=" N VAL A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 removed outlier: 5.918A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 592 through 601 removed outlier: 4.360A pdb=" N GLU A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 618 Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 119 through 144 removed outlier: 4.730A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 Processing helix chain 'B' and resid 194 through 223 removed outlier: 6.599A pdb=" N HIS B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.809A pdb=" N LEU B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.987A pdb=" N LEU B 264 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 4.265A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 304 through 334 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 416 Processing helix chain 'B' and resid 419 through 437 Processing helix chain 'B' and resid 442 through 456 Processing helix chain 'B' and resid 465 through 470 removed outlier: 4.116A pdb=" N VAL B 470 " --> pdb=" O GLN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 490 removed outlier: 5.918A pdb=" N GLU B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 592 through 601 removed outlier: 4.360A pdb=" N GLU B 601 " --> pdb=" O ASN B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 618 Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 119 through 144 removed outlier: 4.730A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 194 through 223 removed outlier: 6.598A pdb=" N HIS C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.791A pdb=" N LEU C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 removed outlier: 3.986A pdb=" N LEU C 264 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 285 removed outlier: 4.265A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 304 through 334 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 416 Processing helix chain 'C' and resid 419 through 437 Processing helix chain 'C' and resid 442 through 456 Processing helix chain 'C' and resid 465 through 470 removed outlier: 4.116A pdb=" N VAL C 470 " --> pdb=" O GLN C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 490 removed outlier: 5.918A pdb=" N GLU C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 592 through 601 removed outlier: 4.361A pdb=" N GLU C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 618 Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 119 through 144 removed outlier: 4.730A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 194 through 223 removed outlier: 6.598A pdb=" N HIS D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 246 Processing helix chain 'D' and resid 249 through 257 removed outlier: 3.818A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.986A pdb=" N LEU D 264 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 285 removed outlier: 4.265A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 304 through 334 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 416 Processing helix chain 'D' and resid 419 through 437 Processing helix chain 'D' and resid 442 through 456 Processing helix chain 'D' and resid 465 through 470 removed outlier: 4.116A pdb=" N VAL D 470 " --> pdb=" O GLN D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 490 removed outlier: 5.918A pdb=" N GLU D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N THR D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 592 through 601 removed outlier: 4.360A pdb=" N GLU D 601 " --> pdb=" O ASN D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 618 Processing sheet with id= A, first strand: chain 'A' and resid 185 through 188 Processing sheet with id= B, first strand: chain 'A' and resid 510 through 514 Processing sheet with id= C, first strand: chain 'A' and resid 550 through 552 removed outlier: 4.155A pdb=" N VAL A 550 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 185 through 188 Processing sheet with id= E, first strand: chain 'B' and resid 510 through 514 Processing sheet with id= F, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.155A pdb=" N VAL B 550 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 185 through 188 Processing sheet with id= H, first strand: chain 'C' and resid 510 through 514 Processing sheet with id= I, first strand: chain 'C' and resid 550 through 552 removed outlier: 4.155A pdb=" N VAL C 550 " --> pdb=" O VAL C 540 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 185 through 188 Processing sheet with id= K, first strand: chain 'D' and resid 510 through 514 Processing sheet with id= L, first strand: chain 'D' and resid 550 through 552 removed outlier: 4.155A pdb=" N VAL D 550 " --> pdb=" O VAL D 540 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2568 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: 4.95 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2676 1.28 - 1.41: 4839 1.41 - 1.54: 10355 1.54 - 1.67: 66 1.67 - 1.81: 156 Bond restraints: 18092 Sorted by residual: bond pdb=" C VAL B 234 " pdb=" O VAL B 234 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.15e-02 7.56e+03 5.82e+01 bond pdb=" C VAL D 234 " pdb=" O VAL D 234 " ideal model delta sigma weight residual 1.237 1.149 0.087 1.15e-02 7.56e+03 5.79e+01 bond pdb=" C ALA B 237 " pdb=" O ALA B 237 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.17e-02 7.31e+03 5.77e+01 bond pdb=" C ALA D 237 " pdb=" O ALA D 237 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.17e-02 7.31e+03 5.75e+01 bond pdb=" C ALA C 237 " pdb=" O ALA C 237 " ideal model delta sigma weight residual 1.237 1.148 0.089 1.17e-02 7.31e+03 5.75e+01 ... (remaining 18087 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.66: 254 105.66 - 112.80: 9850 112.80 - 119.93: 6077 119.93 - 127.07: 7947 127.07 - 134.21: 212 Bond angle restraints: 24340 Sorted by residual: angle pdb=" O3P CPL A 802 " pdb=" P CPL A 802 " pdb=" O4P CPL A 802 " ideal model delta sigma weight residual 93.29 112.53 -19.24 3.00e+00 1.11e-01 4.11e+01 angle pdb=" O3P CPL D 802 " pdb=" P CPL D 802 " pdb=" O4P CPL D 802 " ideal model delta sigma weight residual 93.29 112.52 -19.23 3.00e+00 1.11e-01 4.11e+01 angle pdb=" O3P CPL C 802 " pdb=" P CPL C 802 " pdb=" O4P CPL C 802 " ideal model delta sigma weight residual 93.29 112.51 -19.22 3.00e+00 1.11e-01 4.11e+01 angle pdb=" O3P CPL B 802 " pdb=" P CPL B 802 " pdb=" O4P CPL B 802 " ideal model delta sigma weight residual 93.29 112.49 -19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" N ILE C 563 " pdb=" CA ILE C 563 " pdb=" C ILE C 563 " ideal model delta sigma weight residual 113.42 107.36 6.06 1.17e+00 7.31e-01 2.69e+01 ... (remaining 24335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 10226 29.78 - 59.55: 570 59.55 - 89.33: 40 89.33 - 119.11: 4 119.11 - 148.89: 16 Dihedral angle restraints: 10856 sinusoidal: 4800 harmonic: 6056 Sorted by residual: dihedral pdb=" CA ASP C 191 " pdb=" C ASP C 191 " pdb=" N LEU C 192 " pdb=" CA LEU C 192 " ideal model delta harmonic sigma weight residual 180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ASP A 191 " pdb=" C ASP A 191 " pdb=" N LEU A 192 " pdb=" CA LEU A 192 " ideal model delta harmonic sigma weight residual -180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ASP D 191 " pdb=" C ASP D 191 " pdb=" N LEU D 192 " pdb=" CA LEU D 192 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 10853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2322 0.079 - 0.158: 279 0.158 - 0.237: 7 0.237 - 0.315: 8 0.315 - 0.394: 8 Chirality restraints: 2624 Sorted by residual: chirality pdb=" CA LEU A 257 " pdb=" N LEU A 257 " pdb=" C LEU A 257 " pdb=" CB LEU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA LEU C 257 " pdb=" N LEU C 257 " pdb=" C LEU C 257 " pdb=" CB LEU C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA LEU B 257 " pdb=" N LEU B 257 " pdb=" C LEU B 257 " pdb=" CB LEU B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 2621 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 236 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C GLU C 236 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU C 236 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA C 237 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 236 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C GLU B 236 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU B 236 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 237 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 233 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C VAL A 233 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL A 233 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 234 " 0.018 2.00e-02 2.50e+03 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 349 2.67 - 3.23: 15877 3.23 - 3.78: 27387 3.78 - 4.34: 38967 4.34 - 4.90: 63438 Nonbonded interactions: 146018 Sorted by model distance: nonbonded pdb=" ND2 ASN B 179 " pdb=" O ASP B 353 " model vdw 2.111 2.520 nonbonded pdb=" ND2 ASN D 179 " pdb=" O ASP D 353 " model vdw 2.112 2.520 nonbonded pdb=" ND2 ASN A 179 " pdb=" O ASP A 353 " model vdw 2.112 2.520 nonbonded pdb=" ND2 ASN C 179 " pdb=" O ASP C 353 " model vdw 2.112 2.520 nonbonded pdb=" O ASP D 191 " pdb=" N GLY D 193 " model vdw 2.218 2.520 ... (remaining 146013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 104 through 619 or resid 801 through 809)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.440 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 45.560 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.011 0.089 18092 Z= 0.708 Angle : 1.092 19.240 24340 Z= 0.528 Chirality : 0.057 0.394 2624 Planarity : 0.005 0.047 2956 Dihedral : 17.926 148.885 6956 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.02 % Allowed : 9.27 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.07 (0.16), residues: 2036 helix: -0.96 (0.13), residues: 1176 sheet: -1.19 (0.37), residues: 124 loop : -1.89 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 596 HIS 0.006 0.002 HIS A 321 PHE 0.025 0.003 PHE A 138 TYR 0.025 0.003 TYR A 363 ARG 0.009 0.001 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 282 time to evaluate : 1.995 Fit side-chains REVERT: A 225 MET cc_start: 0.8200 (tpt) cc_final: 0.7979 (tpp) REVERT: A 236 GLU cc_start: 0.6879 (tt0) cc_final: 0.6336 (mp0) REVERT: A 272 ASN cc_start: 0.7699 (m-40) cc_final: 0.6947 (t0) REVERT: A 288 LYS cc_start: 0.7655 (mttt) cc_final: 0.7315 (mttp) REVERT: A 291 ARG cc_start: 0.6808 (mmm160) cc_final: 0.6037 (mtm110) REVERT: A 303 MET cc_start: 0.7165 (mtm) cc_final: 0.6721 (mtp) REVERT: A 417 MET cc_start: 0.8185 (ptp) cc_final: 0.7966 (ptm) REVERT: A 421 ARG cc_start: 0.7428 (tpt170) cc_final: 0.6975 (tpt170) REVERT: A 423 GLU cc_start: 0.6950 (tt0) cc_final: 0.6731 (tt0) REVERT: A 439 LYS cc_start: 0.7442 (mtmm) cc_final: 0.7132 (mtmt) REVERT: A 492 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.8133 (ttp80) REVERT: A 510 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.7061 (mt0) REVERT: A 523 LYS cc_start: 0.7939 (tptm) cc_final: 0.7619 (tptm) REVERT: A 525 ASP cc_start: 0.6637 (t0) cc_final: 0.6416 (m-30) REVERT: A 542 ASP cc_start: 0.7494 (t0) cc_final: 0.7268 (p0) REVERT: B 236 GLU cc_start: 0.7044 (tt0) cc_final: 0.6646 (mp0) REVERT: B 242 LYS cc_start: 0.7556 (ttmt) cc_final: 0.6733 (mmmt) REVERT: B 272 ASN cc_start: 0.7685 (m-40) cc_final: 0.7037 (t0) REVERT: B 288 LYS cc_start: 0.7648 (mttt) cc_final: 0.7302 (mttp) REVERT: B 291 ARG cc_start: 0.6578 (mmm160) cc_final: 0.5868 (mtm110) REVERT: B 303 MET cc_start: 0.7198 (mtm) cc_final: 0.6746 (mtp) REVERT: B 397 MET cc_start: 0.8065 (mtm) cc_final: 0.7810 (mtp) REVERT: B 417 MET cc_start: 0.8292 (ptp) cc_final: 0.7967 (ptm) REVERT: B 421 ARG cc_start: 0.7584 (tpt170) cc_final: 0.7358 (tpt170) REVERT: B 425 GLN cc_start: 0.7156 (tp40) cc_final: 0.6946 (mm-40) REVERT: B 428 MET cc_start: 0.7330 (tpp) cc_final: 0.6945 (tpt) REVERT: B 547 LYS cc_start: 0.7746 (tptm) cc_final: 0.7033 (tptp) REVERT: C 236 GLU cc_start: 0.6683 (tt0) cc_final: 0.5961 (mp0) REVERT: C 272 ASN cc_start: 0.7611 (m-40) cc_final: 0.6916 (t0) REVERT: C 288 LYS cc_start: 0.7662 (mttt) cc_final: 0.7331 (mttp) REVERT: C 291 ARG cc_start: 0.6818 (mmm160) cc_final: 0.6056 (mtm110) REVERT: C 303 MET cc_start: 0.7177 (mtm) cc_final: 0.6797 (mtp) REVERT: C 417 MET cc_start: 0.7958 (ptp) cc_final: 0.7724 (ptm) REVERT: C 421 ARG cc_start: 0.7230 (tpt170) cc_final: 0.6594 (tpt170) REVERT: C 423 GLU cc_start: 0.6856 (tt0) cc_final: 0.6626 (tt0) REVERT: C 425 GLN cc_start: 0.7163 (tp40) cc_final: 0.5840 (mt0) REVERT: C 439 LYS cc_start: 0.7533 (mtmm) cc_final: 0.7251 (mtmt) REVERT: C 458 ASN cc_start: 0.6156 (m110) cc_final: 0.5524 (t0) REVERT: C 523 LYS cc_start: 0.7838 (tptm) cc_final: 0.7492 (tptm) REVERT: C 542 ASP cc_start: 0.7433 (t0) cc_final: 0.7216 (p0) REVERT: C 554 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7474 (mt-10) REVERT: D 236 GLU cc_start: 0.6765 (tt0) cc_final: 0.6004 (mp0) REVERT: D 272 ASN cc_start: 0.7688 (m-40) cc_final: 0.6867 (t0) REVERT: D 288 LYS cc_start: 0.7672 (mttt) cc_final: 0.7247 (mttp) REVERT: D 291 ARG cc_start: 0.6740 (mmm160) cc_final: 0.6005 (mtm110) REVERT: D 303 MET cc_start: 0.7249 (mtm) cc_final: 0.6875 (mtp) REVERT: D 421 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6859 (tpt170) REVERT: D 458 ASN cc_start: 0.6004 (m110) cc_final: 0.5416 (t0) REVERT: D 523 LYS cc_start: 0.7969 (tptm) cc_final: 0.7651 (mmtt) outliers start: 56 outliers final: 19 residues processed: 330 average time/residue: 1.5150 time to fit residues: 551.7929 Evaluate side-chains 272 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 252 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 589 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 120 ASN A 154 GLN A 199 HIS A 409 ASN A 416 ASN A 433 GLN A 443 GLN A 482 GLN A 512 GLN A 539 GLN A 553 GLN B 114 GLN B 120 ASN B 154 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS B 409 ASN B 416 ASN B 433 GLN B 443 GLN B 482 GLN B 512 GLN B 539 GLN B 553 GLN C 114 GLN C 120 ASN C 154 GLN C 199 HIS C 409 ASN C 416 ASN C 443 GLN C 482 GLN C 512 GLN C 539 GLN C 553 GLN C 597 ASN D 114 GLN D 120 ASN D 154 GLN D 199 HIS D 409 ASN D 416 ASN D 443 GLN D 466 GLN D 482 GLN D 512 GLN D 539 GLN D 553 GLN D 597 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18092 Z= 0.170 Angle : 0.494 5.091 24340 Z= 0.267 Chirality : 0.040 0.156 2624 Planarity : 0.004 0.041 2956 Dihedral : 16.277 151.563 2906 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.83 % Allowed : 12.12 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2036 helix: 0.66 (0.14), residues: 1176 sheet: -0.55 (0.39), residues: 124 loop : -1.29 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.004 0.001 HIS C 321 PHE 0.014 0.001 PHE D 328 TYR 0.019 0.001 TYR C 365 ARG 0.002 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 1.857 Fit side-chains REVERT: A 272 ASN cc_start: 0.7675 (m-40) cc_final: 0.6849 (t0) REVERT: A 288 LYS cc_start: 0.7551 (mttt) cc_final: 0.6265 (pmtt) REVERT: A 291 ARG cc_start: 0.6788 (mmm160) cc_final: 0.6002 (mtm110) REVERT: A 303 MET cc_start: 0.6983 (mtm) cc_final: 0.6631 (mtp) REVERT: A 417 MET cc_start: 0.8113 (ptp) cc_final: 0.7883 (ptm) REVERT: A 423 GLU cc_start: 0.6642 (tt0) cc_final: 0.6439 (tt0) REVERT: A 439 LYS cc_start: 0.7523 (mtmm) cc_final: 0.7236 (mtmt) REVERT: A 489 ARG cc_start: 0.7803 (ttt90) cc_final: 0.7595 (tpp-160) REVERT: A 523 LYS cc_start: 0.7880 (tptm) cc_final: 0.7465 (ttmm) REVERT: A 592 LYS cc_start: 0.6468 (tttm) cc_final: 0.6243 (tttt) REVERT: B 146 ASN cc_start: 0.7450 (m-40) cc_final: 0.6997 (m-40) REVERT: B 225 MET cc_start: 0.8207 (tpt) cc_final: 0.8007 (tpp) REVERT: B 236 GLU cc_start: 0.6454 (tt0) cc_final: 0.5934 (mp0) REVERT: B 242 LYS cc_start: 0.7321 (ttmt) cc_final: 0.6519 (mmmt) REVERT: B 272 ASN cc_start: 0.7684 (m-40) cc_final: 0.7040 (t0) REVERT: B 288 LYS cc_start: 0.7507 (mttt) cc_final: 0.6254 (pmtt) REVERT: B 291 ARG cc_start: 0.6700 (mmm160) cc_final: 0.5966 (mtm110) REVERT: B 303 MET cc_start: 0.7035 (mtm) cc_final: 0.6641 (mtp) REVERT: B 417 MET cc_start: 0.8242 (ptp) cc_final: 0.7952 (ptm) REVERT: B 421 ARG cc_start: 0.7520 (tpt170) cc_final: 0.7095 (tpt170) REVERT: B 439 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6967 (mttp) REVERT: B 547 LYS cc_start: 0.7559 (tptm) cc_final: 0.7068 (tptp) REVERT: C 272 ASN cc_start: 0.7669 (m-40) cc_final: 0.6838 (t0) REVERT: C 288 LYS cc_start: 0.7540 (mttt) cc_final: 0.6261 (pmtt) REVERT: C 291 ARG cc_start: 0.6797 (mmm160) cc_final: 0.5993 (mtm110) REVERT: C 303 MET cc_start: 0.6959 (mtm) cc_final: 0.6691 (mtp) REVERT: C 417 MET cc_start: 0.8049 (ptp) cc_final: 0.7840 (ptm) REVERT: C 423 GLU cc_start: 0.6693 (tt0) cc_final: 0.5826 (pt0) REVERT: C 425 GLN cc_start: 0.7127 (tp40) cc_final: 0.5801 (mt0) REVERT: C 523 LYS cc_start: 0.7797 (tptm) cc_final: 0.7515 (tptm) REVERT: C 554 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7553 (mt-10) REVERT: D 211 MET cc_start: 0.7735 (mmt) cc_final: 0.7464 (mmt) REVERT: D 236 GLU cc_start: 0.6274 (tt0) cc_final: 0.5295 (mp0) REVERT: D 272 ASN cc_start: 0.7663 (m-40) cc_final: 0.6775 (t0) REVERT: D 288 LYS cc_start: 0.7587 (mttt) cc_final: 0.7152 (mttp) REVERT: D 291 ARG cc_start: 0.6772 (mmm160) cc_final: 0.6028 (mtm110) REVERT: D 303 MET cc_start: 0.6979 (mtm) cc_final: 0.6738 (mtp) REVERT: D 395 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: D 510 GLN cc_start: 0.7185 (mt0) cc_final: 0.6111 (mm110) REVERT: D 523 LYS cc_start: 0.7845 (tptm) cc_final: 0.7510 (mmtp) outliers start: 34 outliers final: 15 residues processed: 301 average time/residue: 1.4244 time to fit residues: 473.4784 Evaluate side-chains 270 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 253 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 601 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 18092 Z= 0.516 Angle : 0.673 5.673 24340 Z= 0.354 Chirality : 0.049 0.178 2624 Planarity : 0.005 0.038 2956 Dihedral : 16.463 149.913 2888 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.91 % Allowed : 12.55 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.18), residues: 2036 helix: 0.56 (0.14), residues: 1176 sheet: -0.45 (0.38), residues: 124 loop : -1.21 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 596 HIS 0.009 0.003 HIS A 321 PHE 0.026 0.003 PHE C 138 TYR 0.022 0.003 TYR C 363 ARG 0.007 0.001 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 241 time to evaluate : 1.912 Fit side-chains REVERT: A 235 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7915 (mmm160) REVERT: A 236 GLU cc_start: 0.6366 (tt0) cc_final: 0.5601 (mp0) REVERT: A 242 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6647 (mmmt) REVERT: A 272 ASN cc_start: 0.7709 (m-40) cc_final: 0.6970 (t0) REVERT: A 291 ARG cc_start: 0.6824 (mmm160) cc_final: 0.6025 (mtm110) REVERT: A 303 MET cc_start: 0.7064 (mtm) cc_final: 0.6653 (mtp) REVERT: A 417 MET cc_start: 0.8179 (ptp) cc_final: 0.7895 (ptm) REVERT: A 421 ARG cc_start: 0.7409 (tpt170) cc_final: 0.6905 (tpt170) REVERT: A 423 GLU cc_start: 0.6853 (tt0) cc_final: 0.6630 (tt0) REVERT: A 439 LYS cc_start: 0.7284 (mtmm) cc_final: 0.7078 (mtmt) REVERT: A 523 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7686 (tptm) REVERT: B 225 MET cc_start: 0.8239 (tpt) cc_final: 0.8036 (tpp) REVERT: B 235 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7883 (mmm160) REVERT: B 236 GLU cc_start: 0.6455 (tt0) cc_final: 0.5819 (mp0) REVERT: B 272 ASN cc_start: 0.7674 (m-40) cc_final: 0.6965 (t0) REVERT: B 291 ARG cc_start: 0.6827 (mmm160) cc_final: 0.6048 (mtm110) REVERT: B 303 MET cc_start: 0.7074 (mtm) cc_final: 0.6661 (mtp) REVERT: B 417 MET cc_start: 0.8199 (ptp) cc_final: 0.7909 (ptm) REVERT: B 421 ARG cc_start: 0.7535 (tpt170) cc_final: 0.7130 (tpt170) REVERT: B 442 LYS cc_start: 0.6627 (mmtm) cc_final: 0.5932 (mptp) REVERT: B 523 LYS cc_start: 0.8031 (tptm) cc_final: 0.7711 (tptm) REVERT: B 561 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7899 (mp) REVERT: C 235 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7955 (mmm160) REVERT: C 272 ASN cc_start: 0.7708 (m-40) cc_final: 0.6970 (t0) REVERT: C 291 ARG cc_start: 0.6819 (mmm160) cc_final: 0.5990 (mtm110) REVERT: C 303 MET cc_start: 0.7049 (mtm) cc_final: 0.6711 (mtp) REVERT: C 417 MET cc_start: 0.8184 (ptp) cc_final: 0.7910 (ptm) REVERT: C 423 GLU cc_start: 0.6791 (tt0) cc_final: 0.6559 (tt0) REVERT: C 523 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7666 (tptm) REVERT: C 554 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 592 LYS cc_start: 0.6796 (tttm) cc_final: 0.6533 (tttt) REVERT: D 272 ASN cc_start: 0.7674 (m-40) cc_final: 0.6973 (t0) REVERT: D 291 ARG cc_start: 0.6812 (mmm160) cc_final: 0.6058 (mtm180) REVERT: D 303 MET cc_start: 0.7039 (mtm) cc_final: 0.6711 (mtp) REVERT: D 523 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7723 (tptm) REVERT: D 592 LYS cc_start: 0.6829 (tttm) cc_final: 0.6537 (tttt) outliers start: 54 outliers final: 27 residues processed: 276 average time/residue: 1.6655 time to fit residues: 501.9873 Evaluate side-chains 272 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 186 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18092 Z= 0.142 Angle : 0.459 4.763 24340 Z= 0.248 Chirality : 0.039 0.149 2624 Planarity : 0.004 0.041 2956 Dihedral : 15.072 154.209 2887 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.59 % Allowed : 12.72 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.19), residues: 2036 helix: 1.29 (0.15), residues: 1176 sheet: -0.06 (0.38), residues: 124 loop : -0.95 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 124 HIS 0.003 0.001 HIS C 321 PHE 0.013 0.001 PHE C 328 TYR 0.016 0.001 TYR D 365 ARG 0.002 0.000 ARG B 574 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 2.006 Fit side-chains REVERT: A 235 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7887 (mmm-85) REVERT: A 272 ASN cc_start: 0.7727 (m-40) cc_final: 0.6964 (t0) REVERT: A 291 ARG cc_start: 0.6783 (mmm160) cc_final: 0.5946 (mtm110) REVERT: A 303 MET cc_start: 0.6966 (mtm) cc_final: 0.6684 (mtp) REVERT: A 417 MET cc_start: 0.8160 (ptp) cc_final: 0.7908 (ptm) REVERT: A 423 GLU cc_start: 0.6628 (tt0) cc_final: 0.5759 (pt0) REVERT: A 523 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7523 (mmtp) REVERT: A 592 LYS cc_start: 0.6433 (tttm) cc_final: 0.6195 (tttt) REVERT: B 242 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6678 (mmmt) REVERT: B 272 ASN cc_start: 0.7724 (m-40) cc_final: 0.6935 (t0) REVERT: B 291 ARG cc_start: 0.6801 (mmm160) cc_final: 0.6000 (mtm110) REVERT: B 303 MET cc_start: 0.6921 (mtm) cc_final: 0.6629 (mtp) REVERT: B 413 MET cc_start: 0.8405 (ttp) cc_final: 0.8164 (ttp) REVERT: B 417 MET cc_start: 0.8166 (ptp) cc_final: 0.7869 (ptm) REVERT: B 554 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 235 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7866 (mmm-85) REVERT: C 242 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6662 (mmmt) REVERT: C 272 ASN cc_start: 0.7726 (m-40) cc_final: 0.6966 (t0) REVERT: C 291 ARG cc_start: 0.6788 (mmm160) cc_final: 0.5960 (mtm110) REVERT: C 303 MET cc_start: 0.6961 (mtm) cc_final: 0.6670 (mtp) REVERT: C 417 MET cc_start: 0.8159 (ptp) cc_final: 0.7869 (ptm) REVERT: C 423 GLU cc_start: 0.6623 (tt0) cc_final: 0.5762 (pt0) REVERT: C 425 GLN cc_start: 0.7272 (tp40) cc_final: 0.5892 (mt0) REVERT: C 429 ASP cc_start: 0.6763 (m-30) cc_final: 0.6547 (m-30) REVERT: C 510 GLN cc_start: 0.7241 (mt0) cc_final: 0.6109 (mm110) REVERT: C 523 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7505 (tptm) REVERT: C 592 LYS cc_start: 0.6498 (tttm) cc_final: 0.6210 (tttt) REVERT: D 272 ASN cc_start: 0.7728 (m-40) cc_final: 0.6958 (t0) REVERT: D 288 LYS cc_start: 0.7609 (mttt) cc_final: 0.6286 (pmtt) REVERT: D 291 ARG cc_start: 0.6788 (mmm160) cc_final: 0.6019 (mtm180) REVERT: D 303 MET cc_start: 0.6945 (mtm) cc_final: 0.6662 (mtp) REVERT: D 395 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8505 (m-30) REVERT: D 510 GLN cc_start: 0.7178 (mt0) cc_final: 0.6087 (mm110) REVERT: D 523 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7589 (tptm) REVERT: D 592 LYS cc_start: 0.6610 (tttm) cc_final: 0.6337 (tttt) outliers start: 48 outliers final: 19 residues processed: 283 average time/residue: 1.5762 time to fit residues: 488.5693 Evaluate side-chains 270 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 243 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain C residue 235 ARG Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18092 Z= 0.340 Angle : 0.559 5.300 24340 Z= 0.297 Chirality : 0.044 0.162 2624 Planarity : 0.004 0.036 2956 Dihedral : 15.495 153.334 2885 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.86 % Allowed : 13.36 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.18), residues: 2036 helix: 1.14 (0.15), residues: 1176 sheet: -0.07 (0.40), residues: 124 loop : -0.93 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 596 HIS 0.006 0.002 HIS B 321 PHE 0.021 0.002 PHE D 138 TYR 0.018 0.002 TYR C 363 ARG 0.005 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 243 time to evaluate : 1.767 Fit side-chains REVERT: A 242 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.6635 (mmmt) REVERT: A 272 ASN cc_start: 0.7732 (m-40) cc_final: 0.6994 (t0) REVERT: A 291 ARG cc_start: 0.6809 (mmm160) cc_final: 0.5991 (mtm110) REVERT: A 303 MET cc_start: 0.6973 (mtm) cc_final: 0.6680 (mtp) REVERT: A 417 MET cc_start: 0.8191 (ptp) cc_final: 0.7875 (ptm) REVERT: A 423 GLU cc_start: 0.6635 (tt0) cc_final: 0.6420 (tt0) REVERT: A 447 ARG cc_start: 0.6901 (ttt-90) cc_final: 0.6594 (ttt-90) REVERT: A 523 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7687 (tptm) REVERT: A 592 LYS cc_start: 0.6665 (tttm) cc_final: 0.6390 (tttt) REVERT: B 272 ASN cc_start: 0.7723 (m-40) cc_final: 0.6994 (t0) REVERT: B 291 ARG cc_start: 0.6823 (mmm160) cc_final: 0.6043 (mtm110) REVERT: B 303 MET cc_start: 0.6986 (mtm) cc_final: 0.6680 (mtp) REVERT: B 417 MET cc_start: 0.8187 (ptp) cc_final: 0.7871 (ptm) REVERT: B 421 ARG cc_start: 0.7444 (tpt170) cc_final: 0.6948 (tpt170) REVERT: B 442 LYS cc_start: 0.6551 (mmtm) cc_final: 0.5849 (mptp) REVERT: B 447 ARG cc_start: 0.6883 (ttt-90) cc_final: 0.6591 (ttt-90) REVERT: B 561 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7924 (mp) REVERT: C 242 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6643 (mmmt) REVERT: C 272 ASN cc_start: 0.7733 (m-40) cc_final: 0.6997 (t0) REVERT: C 291 ARG cc_start: 0.6807 (mmm160) cc_final: 0.5988 (mtm110) REVERT: C 303 MET cc_start: 0.6964 (mtm) cc_final: 0.6674 (mtp) REVERT: C 417 MET cc_start: 0.8189 (ptp) cc_final: 0.7872 (ptm) REVERT: C 421 ARG cc_start: 0.7391 (tpt170) cc_final: 0.6890 (tpt170) REVERT: C 423 GLU cc_start: 0.6639 (tt0) cc_final: 0.6421 (tt0) REVERT: C 523 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7573 (tptm) REVERT: C 592 LYS cc_start: 0.6714 (tttm) cc_final: 0.6427 (tttt) REVERT: D 242 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6656 (mmmt) REVERT: D 272 ASN cc_start: 0.7623 (m-40) cc_final: 0.6974 (t0) REVERT: D 291 ARG cc_start: 0.6808 (mmm160) cc_final: 0.5997 (mtm110) REVERT: D 303 MET cc_start: 0.6946 (mtm) cc_final: 0.6672 (mtp) REVERT: D 447 ARG cc_start: 0.6941 (ttt-90) cc_final: 0.6640 (ttt-90) REVERT: D 523 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7657 (tptm) REVERT: D 561 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7958 (mp) REVERT: D 592 LYS cc_start: 0.6718 (tttm) cc_final: 0.6443 (tttt) outliers start: 53 outliers final: 32 residues processed: 281 average time/residue: 1.6929 time to fit residues: 518.6651 Evaluate side-chains 276 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 236 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 0.3980 chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18092 Z= 0.191 Angle : 0.478 4.976 24340 Z= 0.257 Chirality : 0.040 0.152 2624 Planarity : 0.004 0.040 2956 Dihedral : 14.927 153.814 2885 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.16 % Allowed : 14.55 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.19), residues: 2036 helix: 1.37 (0.15), residues: 1176 sheet: 0.12 (0.40), residues: 124 loop : -0.84 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.004 0.001 HIS C 321 PHE 0.016 0.002 PHE B 328 TYR 0.017 0.001 TYR A 365 ARG 0.002 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6655 (mmmt) REVERT: A 272 ASN cc_start: 0.7701 (m-40) cc_final: 0.6983 (t0) REVERT: A 291 ARG cc_start: 0.6798 (mmm160) cc_final: 0.5983 (mtm110) REVERT: A 303 MET cc_start: 0.6959 (mtm) cc_final: 0.6660 (mtp) REVERT: A 417 MET cc_start: 0.8156 (ptp) cc_final: 0.7908 (ptm) REVERT: A 423 GLU cc_start: 0.6658 (tt0) cc_final: 0.6450 (tt0) REVERT: A 447 ARG cc_start: 0.6853 (ttt-90) cc_final: 0.6551 (ttt-90) REVERT: A 523 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7617 (tptm) REVERT: A 592 LYS cc_start: 0.6460 (tttm) cc_final: 0.6213 (tttt) REVERT: B 242 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6657 (mmmt) REVERT: B 272 ASN cc_start: 0.7684 (m-40) cc_final: 0.6962 (t0) REVERT: B 291 ARG cc_start: 0.6811 (mmm160) cc_final: 0.6033 (mtm110) REVERT: B 303 MET cc_start: 0.6939 (mtm) cc_final: 0.6629 (mtp) REVERT: B 417 MET cc_start: 0.8145 (ptp) cc_final: 0.7880 (ptm) REVERT: B 442 LYS cc_start: 0.6359 (mmtm) cc_final: 0.5657 (mptp) REVERT: B 592 LYS cc_start: 0.6397 (tttm) cc_final: 0.6148 (tttt) REVERT: C 242 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6664 (mmmt) REVERT: C 272 ASN cc_start: 0.7702 (m-40) cc_final: 0.6985 (t0) REVERT: C 291 ARG cc_start: 0.6798 (mmm160) cc_final: 0.5982 (mtm110) REVERT: C 303 MET cc_start: 0.6954 (mtm) cc_final: 0.6646 (mtp) REVERT: C 417 MET cc_start: 0.8162 (ptp) cc_final: 0.7887 (ptm) REVERT: C 423 GLU cc_start: 0.6669 (tt0) cc_final: 0.6458 (tt0) REVERT: C 425 GLN cc_start: 0.7197 (tp40) cc_final: 0.5805 (mt0) REVERT: C 523 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7620 (tptm) REVERT: C 561 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7953 (mp) REVERT: C 592 LYS cc_start: 0.6645 (tttm) cc_final: 0.6367 (tttt) REVERT: D 242 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6668 (mmmt) REVERT: D 272 ASN cc_start: 0.7641 (m-40) cc_final: 0.6976 (t0) REVERT: D 291 ARG cc_start: 0.6787 (mmm160) cc_final: 0.5974 (mtm110) REVERT: D 303 MET cc_start: 0.6939 (mtm) cc_final: 0.6660 (mtp) REVERT: D 395 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: D 447 ARG cc_start: 0.6829 (ttt-90) cc_final: 0.6544 (ttt-90) REVERT: D 510 GLN cc_start: 0.7214 (mt0) cc_final: 0.6069 (mm110) REVERT: D 523 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7614 (tptm) REVERT: D 561 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7848 (mp) REVERT: D 592 LYS cc_start: 0.6642 (tttm) cc_final: 0.6355 (tttt) outliers start: 40 outliers final: 21 residues processed: 280 average time/residue: 1.5958 time to fit residues: 489.2711 Evaluate side-chains 277 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 246 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 578 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18092 Z= 0.198 Angle : 0.477 5.203 24340 Z= 0.255 Chirality : 0.040 0.152 2624 Planarity : 0.004 0.038 2956 Dihedral : 14.659 154.591 2885 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.64 % Allowed : 14.33 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 2036 helix: 1.46 (0.15), residues: 1176 sheet: 0.27 (0.40), residues: 124 loop : -0.75 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.004 0.002 HIS C 321 PHE 0.016 0.002 PHE A 138 TYR 0.017 0.001 TYR D 365 ARG 0.002 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 258 time to evaluate : 2.015 Fit side-chains revert: symmetry clash REVERT: A 242 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6659 (mmmt) REVERT: A 272 ASN cc_start: 0.7693 (m-40) cc_final: 0.6991 (t0) REVERT: A 274 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7431 (mmm160) REVERT: A 291 ARG cc_start: 0.6759 (mmm160) cc_final: 0.5967 (mtm110) REVERT: A 417 MET cc_start: 0.8144 (ptp) cc_final: 0.7881 (ptm) REVERT: A 421 ARG cc_start: 0.7419 (tpt170) cc_final: 0.6675 (tpt170) REVERT: A 423 GLU cc_start: 0.6661 (tt0) cc_final: 0.5779 (pt0) REVERT: A 425 GLN cc_start: 0.7138 (tp40) cc_final: 0.5791 (mt0) REVERT: A 447 ARG cc_start: 0.6871 (ttt-90) cc_final: 0.6587 (ttt180) REVERT: A 523 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7599 (tptm) REVERT: A 592 LYS cc_start: 0.6607 (tttm) cc_final: 0.6331 (tttt) REVERT: B 242 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6665 (mmmt) REVERT: B 272 ASN cc_start: 0.7674 (m-40) cc_final: 0.6946 (t0) REVERT: B 274 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7432 (mmm160) REVERT: B 291 ARG cc_start: 0.6774 (mmm160) cc_final: 0.6019 (mtm110) REVERT: B 303 MET cc_start: 0.6886 (mtm) cc_final: 0.6656 (mtp) REVERT: B 417 MET cc_start: 0.8141 (ptp) cc_final: 0.7873 (ptm) REVERT: B 421 ARG cc_start: 0.7407 (tpt170) cc_final: 0.6885 (tpt170) REVERT: B 442 LYS cc_start: 0.6305 (mmtm) cc_final: 0.5643 (mptp) REVERT: B 523 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7343 (mmtp) REVERT: B 592 LYS cc_start: 0.6592 (tttm) cc_final: 0.6329 (tttt) REVERT: C 242 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6659 (mmmt) REVERT: C 272 ASN cc_start: 0.7692 (m-40) cc_final: 0.6990 (t0) REVERT: C 274 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7430 (mmm160) REVERT: C 291 ARG cc_start: 0.6762 (mmm160) cc_final: 0.5968 (mtm110) REVERT: C 417 MET cc_start: 0.8140 (ptp) cc_final: 0.7874 (ptm) REVERT: C 421 ARG cc_start: 0.7449 (tpt170) cc_final: 0.6679 (tpt170) REVERT: C 423 GLU cc_start: 0.6668 (tt0) cc_final: 0.5782 (pt0) REVERT: C 425 GLN cc_start: 0.7164 (tp40) cc_final: 0.5791 (mt0) REVERT: C 510 GLN cc_start: 0.7224 (mt0) cc_final: 0.6077 (mm110) REVERT: C 523 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7587 (tptm) REVERT: C 561 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7963 (mp) REVERT: C 592 LYS cc_start: 0.6650 (tttm) cc_final: 0.6368 (tttt) REVERT: D 242 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6667 (mmmt) REVERT: D 272 ASN cc_start: 0.7633 (m-40) cc_final: 0.6967 (t0) REVERT: D 274 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7435 (mmm160) REVERT: D 291 ARG cc_start: 0.6755 (mmm160) cc_final: 0.5995 (mtm110) REVERT: D 395 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8595 (m-30) REVERT: D 442 LYS cc_start: 0.6243 (mmtm) cc_final: 0.5570 (mptp) REVERT: D 447 ARG cc_start: 0.6822 (ttt-90) cc_final: 0.6547 (ttt180) REVERT: D 510 GLN cc_start: 0.7183 (mt0) cc_final: 0.6066 (mm110) REVERT: D 523 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7601 (tptm) REVERT: D 528 ARG cc_start: 0.7437 (ptp-170) cc_final: 0.7200 (ptp-170) REVERT: D 561 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7821 (mp) REVERT: D 592 LYS cc_start: 0.6647 (tttm) cc_final: 0.6354 (tttt) outliers start: 49 outliers final: 27 residues processed: 292 average time/residue: 1.5961 time to fit residues: 510.1780 Evaluate side-chains 282 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 0.0040 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18092 Z= 0.126 Angle : 0.433 5.080 24340 Z= 0.234 Chirality : 0.038 0.149 2624 Planarity : 0.003 0.041 2956 Dihedral : 14.203 154.676 2885 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.19), residues: 2036 helix: 1.52 (0.15), residues: 1200 sheet: 0.57 (0.41), residues: 124 loop : -0.69 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 124 HIS 0.003 0.001 HIS A 321 PHE 0.013 0.001 PHE A 328 TYR 0.015 0.001 TYR D 365 ARG 0.002 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6617 (mmmt) REVERT: A 272 ASN cc_start: 0.7654 (m-40) cc_final: 0.6944 (t0) REVERT: A 291 ARG cc_start: 0.6755 (mmm160) cc_final: 0.5927 (mtm110) REVERT: A 417 MET cc_start: 0.8114 (ptp) cc_final: 0.7872 (ptm) REVERT: A 423 GLU cc_start: 0.6638 (tt0) cc_final: 0.5788 (pt0) REVERT: A 425 GLN cc_start: 0.7168 (tp40) cc_final: 0.5821 (mt0) REVERT: A 510 GLN cc_start: 0.7093 (mt0) cc_final: 0.6066 (mm110) REVERT: A 523 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7530 (tptm) REVERT: A 592 LYS cc_start: 0.6419 (tttm) cc_final: 0.6165 (tttt) REVERT: B 242 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6621 (mmmt) REVERT: B 272 ASN cc_start: 0.7695 (m-40) cc_final: 0.6918 (t0) REVERT: B 291 ARG cc_start: 0.6776 (mmm160) cc_final: 0.5999 (mtm110) REVERT: B 417 MET cc_start: 0.8122 (ptp) cc_final: 0.7886 (ptm) REVERT: B 510 GLN cc_start: 0.7199 (mt0) cc_final: 0.6051 (mm110) REVERT: B 523 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7303 (mmtp) REVERT: B 592 LYS cc_start: 0.6383 (tttm) cc_final: 0.6138 (tttt) REVERT: C 242 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6541 (mmmt) REVERT: C 246 GLN cc_start: 0.7565 (mm110) cc_final: 0.7271 (mp-120) REVERT: C 272 ASN cc_start: 0.7655 (m-40) cc_final: 0.6943 (t0) REVERT: C 291 ARG cc_start: 0.6760 (mmm160) cc_final: 0.5929 (mtm110) REVERT: C 417 MET cc_start: 0.8139 (ptp) cc_final: 0.7889 (ptm) REVERT: C 423 GLU cc_start: 0.6647 (tt0) cc_final: 0.5790 (pt0) REVERT: C 425 GLN cc_start: 0.7171 (tp40) cc_final: 0.5833 (mt0) REVERT: C 442 LYS cc_start: 0.6221 (mmtm) cc_final: 0.5553 (mptp) REVERT: C 510 GLN cc_start: 0.7189 (mt0) cc_final: 0.6092 (mm110) REVERT: C 523 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7559 (mmtp) REVERT: C 561 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7871 (mp) REVERT: C 592 LYS cc_start: 0.6607 (tttm) cc_final: 0.6321 (tttt) REVERT: D 242 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6678 (mmmt) REVERT: D 272 ASN cc_start: 0.7585 (m-40) cc_final: 0.6927 (t0) REVERT: D 291 ARG cc_start: 0.6754 (mmm160) cc_final: 0.5973 (mtm110) REVERT: D 395 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8488 (m-30) REVERT: D 442 LYS cc_start: 0.6194 (mmtm) cc_final: 0.5545 (mptp) REVERT: D 489 ARG cc_start: 0.7818 (ttt90) cc_final: 0.7460 (tpt170) REVERT: D 510 GLN cc_start: 0.7170 (mt0) cc_final: 0.6043 (mm110) REVERT: D 523 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7537 (tptm) REVERT: D 528 ARG cc_start: 0.7476 (ptp-170) cc_final: 0.7241 (ptp-170) REVERT: D 592 LYS cc_start: 0.6564 (tttm) cc_final: 0.6277 (tttt) outliers start: 48 outliers final: 26 residues processed: 295 average time/residue: 1.5250 time to fit residues: 494.0501 Evaluate side-chains 286 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18092 Z= 0.159 Angle : 0.450 5.410 24340 Z= 0.241 Chirality : 0.039 0.163 2624 Planarity : 0.003 0.039 2956 Dihedral : 14.165 154.312 2885 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.10 % Allowed : 15.41 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.19), residues: 2036 helix: 1.53 (0.15), residues: 1200 sheet: 0.67 (0.41), residues: 124 loop : -0.65 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 124 HIS 0.003 0.001 HIS D 321 PHE 0.015 0.001 PHE A 328 TYR 0.016 0.001 TYR D 365 ARG 0.002 0.000 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 253 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASN cc_start: 0.7579 (m-40) cc_final: 0.6926 (t0) REVERT: A 291 ARG cc_start: 0.6750 (mmm160) cc_final: 0.5971 (mtm110) REVERT: A 417 MET cc_start: 0.8134 (ptp) cc_final: 0.7885 (ptm) REVERT: A 423 GLU cc_start: 0.6656 (tt0) cc_final: 0.5802 (pt0) REVERT: A 425 GLN cc_start: 0.7163 (tp40) cc_final: 0.5828 (mt0) REVERT: A 510 GLN cc_start: 0.7087 (mt0) cc_final: 0.6047 (mm110) REVERT: A 523 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7516 (mmtp) REVERT: A 592 LYS cc_start: 0.6576 (tttm) cc_final: 0.6307 (tttt) REVERT: B 242 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6653 (mmmt) REVERT: B 272 ASN cc_start: 0.7684 (m-40) cc_final: 0.6910 (t0) REVERT: B 291 ARG cc_start: 0.6779 (mmm160) cc_final: 0.5999 (mtm110) REVERT: B 417 MET cc_start: 0.8132 (ptp) cc_final: 0.7890 (ptm) REVERT: B 510 GLN cc_start: 0.7200 (mt0) cc_final: 0.6055 (mm110) REVERT: B 523 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7309 (mmtp) REVERT: B 592 LYS cc_start: 0.6588 (tttm) cc_final: 0.6329 (tttt) REVERT: C 242 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6648 (mmmt) REVERT: C 272 ASN cc_start: 0.7579 (m-40) cc_final: 0.6926 (t0) REVERT: C 291 ARG cc_start: 0.6756 (mmm160) cc_final: 0.5972 (mtm110) REVERT: C 417 MET cc_start: 0.8127 (ptp) cc_final: 0.7886 (ptm) REVERT: C 423 GLU cc_start: 0.6632 (tt0) cc_final: 0.5773 (pt0) REVERT: C 425 GLN cc_start: 0.7158 (tp40) cc_final: 0.5829 (mt0) REVERT: C 442 LYS cc_start: 0.6230 (mmtm) cc_final: 0.5559 (mptp) REVERT: C 510 GLN cc_start: 0.7186 (mt0) cc_final: 0.6127 (mm110) REVERT: C 523 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7667 (mmtp) REVERT: C 561 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7843 (mp) REVERT: C 592 LYS cc_start: 0.6619 (tttm) cc_final: 0.6344 (tttt) REVERT: D 242 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6687 (mmmt) REVERT: D 272 ASN cc_start: 0.7581 (m-40) cc_final: 0.6921 (t0) REVERT: D 291 ARG cc_start: 0.6758 (mmm160) cc_final: 0.5991 (mtm110) REVERT: D 395 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8536 (m-30) REVERT: D 442 LYS cc_start: 0.6207 (mmtm) cc_final: 0.5555 (mptp) REVERT: D 489 ARG cc_start: 0.7823 (ttt90) cc_final: 0.7470 (tpt170) REVERT: D 510 GLN cc_start: 0.7144 (mt0) cc_final: 0.6104 (mm110) REVERT: D 523 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7530 (mmtp) REVERT: D 528 ARG cc_start: 0.7466 (ptp-170) cc_final: 0.7231 (ptp-170) REVERT: D 592 LYS cc_start: 0.6563 (tttm) cc_final: 0.6282 (tttt) outliers start: 39 outliers final: 24 residues processed: 278 average time/residue: 1.5875 time to fit residues: 488.4325 Evaluate side-chains 282 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 249 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18092 Z= 0.202 Angle : 0.484 5.925 24340 Z= 0.257 Chirality : 0.040 0.177 2624 Planarity : 0.004 0.039 2956 Dihedral : 14.293 153.632 2885 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.89 % Allowed : 15.62 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.19), residues: 2036 helix: 1.59 (0.15), residues: 1176 sheet: 0.53 (0.41), residues: 124 loop : -0.63 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 596 HIS 0.004 0.002 HIS C 321 PHE 0.017 0.002 PHE D 138 TYR 0.017 0.001 TYR D 365 ARG 0.002 0.000 ARG D 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4072 Ramachandran restraints generated. 2036 Oldfield, 0 Emsley, 2036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASN cc_start: 0.7617 (m-40) cc_final: 0.6962 (t0) REVERT: A 291 ARG cc_start: 0.6760 (mmm160) cc_final: 0.5995 (mtm110) REVERT: A 417 MET cc_start: 0.8149 (ptp) cc_final: 0.7888 (ptm) REVERT: A 423 GLU cc_start: 0.6660 (tt0) cc_final: 0.5782 (pt0) REVERT: A 425 GLN cc_start: 0.7163 (tp40) cc_final: 0.5829 (mt0) REVERT: A 523 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7552 (tptm) REVERT: A 592 LYS cc_start: 0.6616 (tttm) cc_final: 0.6338 (tttt) REVERT: B 272 ASN cc_start: 0.7597 (m-40) cc_final: 0.6940 (t0) REVERT: B 291 ARG cc_start: 0.6784 (mmm160) cc_final: 0.6019 (mtm110) REVERT: B 417 MET cc_start: 0.8132 (ptp) cc_final: 0.7870 (ptm) REVERT: B 421 ARG cc_start: 0.7400 (tpt170) cc_final: 0.6868 (tpt170) REVERT: B 523 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7312 (mmtp) REVERT: B 592 LYS cc_start: 0.6607 (tttm) cc_final: 0.6343 (tttt) REVERT: C 242 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6627 (mmmt) REVERT: C 272 ASN cc_start: 0.7616 (m-40) cc_final: 0.6960 (t0) REVERT: C 291 ARG cc_start: 0.6745 (mmm160) cc_final: 0.5984 (mtm110) REVERT: C 417 MET cc_start: 0.8129 (ptp) cc_final: 0.7866 (ptm) REVERT: C 421 ARG cc_start: 0.7418 (tpt170) cc_final: 0.6716 (tpt170) REVERT: C 423 GLU cc_start: 0.6662 (tt0) cc_final: 0.5781 (pt0) REVERT: C 425 GLN cc_start: 0.7170 (tp40) cc_final: 0.5861 (mt0) REVERT: C 442 LYS cc_start: 0.6248 (mmtm) cc_final: 0.5576 (mptp) REVERT: C 447 ARG cc_start: 0.6800 (ttt-90) cc_final: 0.6529 (ttt180) REVERT: C 523 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7432 (mmtp) REVERT: C 592 LYS cc_start: 0.6654 (tttm) cc_final: 0.6370 (tttt) REVERT: D 242 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6619 (mmmt) REVERT: D 272 ASN cc_start: 0.7619 (m-40) cc_final: 0.6961 (t0) REVERT: D 291 ARG cc_start: 0.6763 (mmm160) cc_final: 0.5996 (mtm110) REVERT: D 395 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: D 447 ARG cc_start: 0.6801 (ttt-90) cc_final: 0.6537 (ttt180) REVERT: D 489 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7517 (tpt170) REVERT: D 510 GLN cc_start: 0.7117 (mt0) cc_final: 0.6115 (mm110) REVERT: D 523 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7530 (mmtp) REVERT: D 528 ARG cc_start: 0.7467 (ptp-170) cc_final: 0.7232 (ptp-170) REVERT: D 592 LYS cc_start: 0.6653 (tttm) cc_final: 0.6361 (tttt) outliers start: 35 outliers final: 28 residues processed: 276 average time/residue: 1.5975 time to fit residues: 482.5033 Evaluate side-chains 286 residues out of total 1856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 523 LYS Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 601 GLU Chi-restraints excluded: chain C residue 609 LEU Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 481 MET Chi-restraints excluded: chain D residue 523 LYS Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain D residue 601 GLU Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115075 restraints weight = 17092.021| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.87 r_work: 0.3431 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18092 Z= 0.184 Angle : 0.474 5.792 24340 Z= 0.252 Chirality : 0.040 0.152 2624 Planarity : 0.004 0.039 2956 Dihedral : 14.231 153.184 2885 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.10 % Allowed : 15.41 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.19), residues: 2036 helix: 1.62 (0.15), residues: 1176 sheet: 0.59 (0.41), residues: 124 loop : -0.61 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 596 HIS 0.004 0.001 HIS C 321 PHE 0.015 0.002 PHE B 328 TYR 0.016 0.001 TYR D 365 ARG 0.002 0.000 ARG B 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8022.20 seconds wall clock time: 143 minutes 37.89 seconds (8617.89 seconds total)