Starting phenix.real_space_refine on Mon Mar 11 11:46:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8et8_28588/03_2024/8et8_28588_trim_updated.pdb" } resolution = 3.45 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= 0.039 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 2708 2.51 5 N 671 2.21 5 O 710 1.98 5 H 4007 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8125 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8064 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 25, 'TRANS': 506} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'4YH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.53 Number of scatterers: 8125 At special positions: 0 Unit cell: (113.52, 58.96, 72.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 710 8.00 N 671 7.00 C 2708 6.00 H 4007 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.02 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=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 71 " Time building additional restraints: 6.71 Conformation dependent library (CDL) restraints added in 899.9 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 0 sheets defined 68.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 16 through 37 removed outlier: 3.500A pdb=" N LEU A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 53 through 61 removed outlier: 4.080A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.555A pdb=" N CYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 145 through 173 removed outlier: 4.351A pdb=" N VAL A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 169 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 172 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 195 removed outlier: 3.539A pdb=" N THR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 removed outlier: 4.354A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 257 Processing helix chain 'A' and resid 261 through 280 Proline residue: A 271 - end of helix removed outlier: 4.268A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 315 through 319 removed outlier: 4.032A pdb=" N LYS A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 375 through 400 removed outlier: 3.996A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.653A pdb=" N THR A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 490 removed outlier: 4.066A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.867A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.071A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 228 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3998 1.03 - 1.23: 12 1.23 - 1.42: 1771 1.42 - 1.62: 2410 1.62 - 1.81: 43 Bond restraints: 8234 Sorted by residual: bond pdb=" C1 4YH A 601 " pdb=" C3 4YH A 601 " ideal model delta sigma weight residual 1.527 1.484 0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C13 4YH A 601 " pdb=" C9 4YH A 601 " ideal model delta sigma weight residual 1.385 1.354 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C6 4YH A 601 " pdb=" C9 4YH A 601 " ideal model delta sigma weight residual 1.385 1.356 0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 8229 not shown) Histogram of bond angle deviations from ideal: 98.46 - 114.09: 9832 114.09 - 129.72: 4977 129.72 - 145.34: 35 145.34 - 160.97: 0 160.97 - 176.60: 1 Bond angle restraints: 14845 Sorted by residual: angle pdb=" C16 4YH A 601 " pdb=" C21 4YH A 601 " pdb=" C17 4YH A 601 " ideal model delta sigma weight residual 109.48 121.80 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 111.77 108.47 3.30 1.04e+00 9.25e-01 1.01e+01 angle pdb=" C22 4YH A 601 " pdb=" C1 4YH A 601 " pdb=" C3 4YH A 601 " ideal model delta sigma weight residual 109.46 101.29 8.17 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C15 4YH A 601 " pdb=" C1 4YH A 601 " pdb=" C22 4YH A 601 " ideal model delta sigma weight residual 109.47 117.27 -7.80 3.00e+00 1.11e-01 6.75e+00 angle pdb=" C1 4YH A 601 " pdb=" C22 4YH A 601 " pdb=" C26 4YH A 601 " ideal model delta sigma weight residual 109.47 116.83 -7.36 3.00e+00 1.11e-01 6.02e+00 ... (remaining 14840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.79: 3663 18.79 - 37.58: 184 37.58 - 56.36: 82 56.36 - 75.15: 14 75.15 - 93.94: 3 Dihedral angle restraints: 3946 sinusoidal: 2090 harmonic: 1856 Sorted by residual: dihedral pdb=" C21 4YH A 601 " pdb=" C16 4YH A 601 " pdb=" N8 4YH A 601 " pdb=" C25 4YH A 601 " ideal model delta sinusoidal sigma weight residual -156.72 -62.78 -93.94 1 3.00e+01 1.11e-03 1.14e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 64.91 28.09 1 1.00e+01 1.00e-02 1.13e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -110.82 24.82 1 1.00e+01 1.00e-02 8.87e+00 ... (remaining 3943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 665 0.096 - 0.191: 9 0.191 - 0.287: 0 0.287 - 0.382: 0 0.382 - 0.478: 1 Chirality restraints: 675 Sorted by residual: chirality pdb=" C1 4YH A 601 " pdb=" C15 4YH A 601 " pdb=" C2 4YH A 601 " pdb=" C22 4YH A 601 " both_signs ideal model delta sigma weight residual False 2.74 2.27 0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 7.21e-01 chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 672 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 75 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 271 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 4YH A 601 " -0.000 2.00e-02 2.50e+03 8.14e-03 1.49e+00 pdb=" C12 4YH A 601 " 0.008 2.00e-02 2.50e+03 pdb=" C14 4YH A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C17 4YH A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C18 4YH A 601 " 0.006 2.00e-02 2.50e+03 pdb=" C21 4YH A 601 " -0.015 2.00e-02 2.50e+03 pdb=" C7 4YH A 601 " 0.011 2.00e-02 2.50e+03 pdb=" O20 4YH A 601 " -0.005 2.00e-02 2.50e+03 pdb=" O24 4YH A 601 " -0.011 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 310 2.17 - 2.78: 15665 2.78 - 3.39: 22686 3.39 - 3.99: 27496 3.99 - 4.60: 43235 Nonbonded interactions: 109392 Sorted by model distance: nonbonded pdb="HH21 ARG A 233 " pdb=" OE2 GLU A 455 " model vdw 1.564 1.850 nonbonded pdb=" HE ARG A 234 " pdb=" OD2 ASP A 398 " model vdw 1.647 1.850 nonbonded pdb=" O CYS A 26 " pdb=" HG SER A 29 " model vdw 1.752 1.850 nonbonded pdb=" OG1 THR A 347 " pdb=" HH TYR A 457 " model vdw 1.761 1.850 nonbonded pdb=" O VAL A 249 " pdb=" HG SER A 252 " model vdw 1.798 1.850 ... (remaining 109387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 3.710 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.830 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 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 : 0.003 0.043 4227 Z= 0.212 Angle : 0.597 12.321 5770 Z= 0.291 Chirality : 0.038 0.478 675 Planarity : 0.004 0.034 709 Dihedral : 11.861 93.941 1486 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.94 % Allowed : 4.25 % Favored : 94.81 % 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: 1.27 (0.37), residues: 530 helix: 1.73 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.06 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 304 PHE 0.010 0.001 PHE A 275 TYR 0.015 0.001 TYR A 72 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8385 (tp) cc_final: 0.7822 (mt) REVERT: A 242 MET cc_start: 0.6546 (ttt) cc_final: 0.6256 (mtp) REVERT: A 360 LEU cc_start: 0.8556 (tp) cc_final: 0.8084 (tp) REVERT: A 393 ILE cc_start: 0.8876 (tt) cc_final: 0.8450 (tt) REVERT: A 457 TYR cc_start: 0.8361 (m-80) cc_final: 0.8084 (m-80) outliers start: 4 outliers final: 4 residues processed: 112 average time/residue: 0.3152 time to fit residues: 45.2390 Evaluate side-chains 81 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 178 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 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 292 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4227 Z= 0.210 Angle : 0.559 7.341 5770 Z= 0.301 Chirality : 0.034 0.134 675 Planarity : 0.005 0.041 709 Dihedral : 7.566 92.273 630 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.12 % Allowed : 12.74 % Favored : 85.14 % 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: 1.00 (0.37), residues: 530 helix: 1.53 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -1.21 (0.49), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 217 HIS 0.004 0.001 HIS A 304 PHE 0.009 0.001 PHE A 275 TYR 0.012 0.001 TYR A 199 ARG 0.007 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8791 (tt) cc_final: 0.8338 (mm) REVERT: A 180 LEU cc_start: 0.8402 (tp) cc_final: 0.7873 (mt) REVERT: A 242 MET cc_start: 0.6529 (ttt) cc_final: 0.6209 (mtp) REVERT: A 333 SER cc_start: 0.8356 (t) cc_final: 0.7917 (m) REVERT: A 360 LEU cc_start: 0.8578 (tp) cc_final: 0.8077 (tp) REVERT: A 457 TYR cc_start: 0.8405 (m-80) cc_final: 0.8121 (m-80) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.2382 time to fit residues: 26.9490 Evaluate side-chains 76 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 0.0000 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4227 Z= 0.191 Angle : 0.523 5.272 5770 Z= 0.281 Chirality : 0.034 0.134 675 Planarity : 0.005 0.045 709 Dihedral : 7.122 81.071 629 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.12 % Allowed : 13.44 % Favored : 84.43 % 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: 0.84 (0.37), residues: 530 helix: 1.45 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -1.35 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 217 HIS 0.003 0.001 HIS A 304 PHE 0.008 0.001 PHE A 275 TYR 0.011 0.001 TYR A 199 ARG 0.005 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8368 (tp) cc_final: 0.7871 (mt) REVERT: A 242 MET cc_start: 0.6572 (ttt) cc_final: 0.6233 (mtp) REVERT: A 333 SER cc_start: 0.8331 (t) cc_final: 0.7877 (m) REVERT: A 360 LEU cc_start: 0.8487 (tp) cc_final: 0.7972 (tp) REVERT: A 457 TYR cc_start: 0.8460 (m-80) cc_final: 0.8164 (m-80) REVERT: A 497 ILE cc_start: 0.8044 (mm) cc_final: 0.7776 (mt) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.2294 time to fit residues: 24.3050 Evaluate side-chains 76 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 484 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4227 Z= 0.191 Angle : 0.504 5.825 5770 Z= 0.271 Chirality : 0.033 0.132 675 Planarity : 0.005 0.044 709 Dihedral : 7.036 76.749 629 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.59 % Allowed : 13.92 % Favored : 83.49 % 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: 0.81 (0.37), residues: 530 helix: 1.40 (0.28), residues: 358 sheet: None (None), residues: 0 loop : -1.30 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 PHE 0.007 0.001 PHE A 380 TYR 0.010 0.001 TYR A 199 ARG 0.004 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8367 (tp) cc_final: 0.7881 (mt) REVERT: A 242 MET cc_start: 0.6533 (ttt) cc_final: 0.6191 (mtp) REVERT: A 333 SER cc_start: 0.8337 (t) cc_final: 0.7847 (m) REVERT: A 360 LEU cc_start: 0.8524 (tp) cc_final: 0.8074 (mt) REVERT: A 457 TYR cc_start: 0.8475 (m-80) cc_final: 0.8166 (m-80) REVERT: A 497 ILE cc_start: 0.8076 (mm) cc_final: 0.7819 (mt) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.2334 time to fit residues: 25.5306 Evaluate side-chains 80 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 484 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4227 Z= 0.269 Angle : 0.561 6.668 5770 Z= 0.304 Chirality : 0.036 0.127 675 Planarity : 0.005 0.068 709 Dihedral : 7.072 79.944 627 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.59 % Allowed : 15.57 % Favored : 81.84 % 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: 0.35 (0.37), residues: 530 helix: 1.00 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 217 HIS 0.002 0.001 HIS A 304 PHE 0.011 0.001 PHE A 380 TYR 0.011 0.002 TYR A 240 ARG 0.009 0.001 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7684 (mp0) cc_final: 0.7283 (mp0) REVERT: A 180 LEU cc_start: 0.8363 (tp) cc_final: 0.7891 (mt) REVERT: A 227 PHE cc_start: 0.7739 (m-80) cc_final: 0.7534 (m-10) REVERT: A 242 MET cc_start: 0.6581 (ttt) cc_final: 0.6220 (mtp) REVERT: A 360 LEU cc_start: 0.8626 (tp) cc_final: 0.8202 (mt) REVERT: A 457 TYR cc_start: 0.8564 (m-80) cc_final: 0.8222 (m-80) REVERT: A 497 ILE cc_start: 0.8189 (mm) cc_final: 0.7952 (mt) REVERT: A 504 LEU cc_start: 0.8348 (tt) cc_final: 0.8073 (tt) outliers start: 11 outliers final: 10 residues processed: 77 average time/residue: 0.2319 time to fit residues: 24.4982 Evaluate side-chains 79 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 484 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4227 Z= 0.213 Angle : 0.521 6.483 5770 Z= 0.278 Chirality : 0.034 0.128 675 Planarity : 0.005 0.055 709 Dihedral : 7.014 78.215 627 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.07 % Allowed : 16.98 % Favored : 79.95 % 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: 0.48 (0.37), residues: 530 helix: 1.12 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.36 (0.48), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.002 0.001 HIS A 304 PHE 0.008 0.001 PHE A 380 TYR 0.008 0.001 TYR A 279 ARG 0.007 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7777 (mp0) cc_final: 0.7322 (mp0) REVERT: A 180 LEU cc_start: 0.8362 (tp) cc_final: 0.7903 (mt) REVERT: A 227 PHE cc_start: 0.7723 (m-80) cc_final: 0.7463 (m-10) REVERT: A 242 MET cc_start: 0.6534 (ttt) cc_final: 0.6179 (mtp) REVERT: A 360 LEU cc_start: 0.8644 (tp) cc_final: 0.8230 (mt) REVERT: A 457 TYR cc_start: 0.8563 (m-80) cc_final: 0.8214 (m-80) REVERT: A 497 ILE cc_start: 0.8189 (mm) cc_final: 0.7954 (mt) REVERT: A 504 LEU cc_start: 0.8356 (tt) cc_final: 0.8092 (tt) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.2394 time to fit residues: 24.9402 Evaluate side-chains 79 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 483 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4227 Z= 0.187 Angle : 0.503 5.909 5770 Z= 0.265 Chirality : 0.034 0.127 675 Planarity : 0.005 0.065 709 Dihedral : 6.872 77.585 627 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.36 % Allowed : 17.45 % Favored : 80.19 % 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: 0.61 (0.38), residues: 530 helix: 1.23 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.33 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.002 0.001 HIS A 367 PHE 0.007 0.001 PHE A 380 TYR 0.009 0.001 TYR A 240 ARG 0.009 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7793 (mp0) cc_final: 0.7342 (mp0) REVERT: A 180 LEU cc_start: 0.8331 (tp) cc_final: 0.7894 (mt) REVERT: A 227 PHE cc_start: 0.7717 (m-80) cc_final: 0.7393 (m-10) REVERT: A 242 MET cc_start: 0.6499 (ttt) cc_final: 0.6141 (mtp) REVERT: A 360 LEU cc_start: 0.8621 (tp) cc_final: 0.8216 (mt) REVERT: A 440 MET cc_start: 0.6002 (ttp) cc_final: 0.5700 (mtp) REVERT: A 457 TYR cc_start: 0.8524 (m-80) cc_final: 0.8175 (m-80) REVERT: A 497 ILE cc_start: 0.8116 (mm) cc_final: 0.7897 (mt) REVERT: A 504 LEU cc_start: 0.8396 (tt) cc_final: 0.8137 (tt) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.2694 time to fit residues: 28.0813 Evaluate side-chains 79 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 397 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.0050 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4227 Z= 0.146 Angle : 0.490 5.944 5770 Z= 0.254 Chirality : 0.033 0.125 675 Planarity : 0.005 0.057 709 Dihedral : 6.672 74.910 627 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.12 % Allowed : 17.92 % Favored : 79.95 % 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: 0.79 (0.38), residues: 530 helix: 1.37 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.28 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.002 0.000 HIS A 367 PHE 0.006 0.001 PHE A 275 TYR 0.008 0.001 TYR A 72 ARG 0.009 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7752 (mp0) cc_final: 0.7319 (mp0) REVERT: A 180 LEU cc_start: 0.8300 (tp) cc_final: 0.7872 (mt) REVERT: A 242 MET cc_start: 0.6465 (ttt) cc_final: 0.6118 (mtp) REVERT: A 360 LEU cc_start: 0.8618 (tp) cc_final: 0.8211 (mt) REVERT: A 457 TYR cc_start: 0.8514 (m-80) cc_final: 0.8168 (m-80) REVERT: A 497 ILE cc_start: 0.8110 (mm) cc_final: 0.7895 (mt) REVERT: A 504 LEU cc_start: 0.8395 (tt) cc_final: 0.8138 (tt) outliers start: 9 outliers final: 8 residues processed: 76 average time/residue: 0.2538 time to fit residues: 25.9615 Evaluate side-chains 78 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 397 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4227 Z= 0.174 Angle : 0.494 5.758 5770 Z= 0.259 Chirality : 0.033 0.124 675 Planarity : 0.005 0.066 709 Dihedral : 6.601 76.961 627 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.12 % Allowed : 16.98 % Favored : 80.90 % 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: 0.70 (0.38), residues: 530 helix: 1.24 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.24 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.002 0.001 HIS A 367 PHE 0.006 0.001 PHE A 380 TYR 0.008 0.001 TYR A 72 ARG 0.009 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7782 (mp0) cc_final: 0.7374 (mp0) REVERT: A 180 LEU cc_start: 0.8321 (tp) cc_final: 0.7904 (mt) REVERT: A 227 PHE cc_start: 0.7725 (m-80) cc_final: 0.7427 (m-10) REVERT: A 242 MET cc_start: 0.6495 (ttt) cc_final: 0.6128 (mtp) REVERT: A 360 LEU cc_start: 0.8643 (tp) cc_final: 0.8248 (mt) REVERT: A 457 TYR cc_start: 0.8524 (m-80) cc_final: 0.8183 (m-80) REVERT: A 497 ILE cc_start: 0.8085 (mm) cc_final: 0.7878 (mt) REVERT: A 504 LEU cc_start: 0.8396 (tt) cc_final: 0.8138 (tt) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.2534 time to fit residues: 25.5746 Evaluate side-chains 79 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 397 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 0.0470 chunk 4 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4227 Z= 0.136 Angle : 0.480 6.037 5770 Z= 0.247 Chirality : 0.033 0.123 675 Planarity : 0.005 0.059 709 Dihedral : 6.395 74.237 627 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.89 % Allowed : 17.92 % Favored : 80.19 % 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: 0.88 (0.38), residues: 530 helix: 1.38 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.19 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 429 HIS 0.002 0.000 HIS A 367 PHE 0.006 0.001 PHE A 275 TYR 0.008 0.001 TYR A 72 ARG 0.008 0.000 ARG A 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7739 (mp0) cc_final: 0.7349 (mp0) REVERT: A 180 LEU cc_start: 0.8291 (tp) cc_final: 0.7802 (mt) REVERT: A 227 PHE cc_start: 0.7710 (m-80) cc_final: 0.7387 (m-10) REVERT: A 242 MET cc_start: 0.6463 (ttt) cc_final: 0.6104 (mtp) REVERT: A 360 LEU cc_start: 0.8594 (tp) cc_final: 0.8191 (mt) REVERT: A 457 TYR cc_start: 0.8502 (m-80) cc_final: 0.8157 (m-80) REVERT: A 483 LEU cc_start: 0.8470 (tp) cc_final: 0.7997 (tt) REVERT: A 497 ILE cc_start: 0.7969 (mm) cc_final: 0.7761 (mt) REVERT: A 504 LEU cc_start: 0.8398 (tt) cc_final: 0.8141 (tt) outliers start: 8 outliers final: 8 residues processed: 77 average time/residue: 0.2586 time to fit residues: 26.6814 Evaluate side-chains 80 residues out of total 448 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 397 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.183190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147590 restraints weight = 12863.814| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.07 r_work: 0.3479 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4227 Z= 0.170 Angle : 0.490 6.108 5770 Z= 0.255 Chirality : 0.033 0.123 675 Planarity : 0.005 0.058 709 Dihedral : 6.416 76.355 627 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.89 % Allowed : 17.69 % Favored : 80.42 % 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: 0.76 (0.38), residues: 530 helix: 1.30 (0.28), residues: 363 sheet: None (None), residues: 0 loop : -1.25 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 429 HIS 0.002 0.001 HIS A 367 PHE 0.006 0.001 PHE A 275 TYR 0.008 0.001 TYR A 72 ARG 0.008 0.000 ARG A 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.07 seconds wall clock time: 49 minutes 41.04 seconds (2981.04 seconds total)