Starting phenix.real_space_refine on Fri Dec 27 09:28:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjg_37579/12_2024/8wjg_37579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjg_37579/12_2024/8wjg_37579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wjg_37579/12_2024/8wjg_37579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjg_37579/12_2024/8wjg_37579.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjg_37579/12_2024/8wjg_37579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjg_37579/12_2024/8wjg_37579.cif" } resolution = 3.0 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= 0.004 sd= 0.167 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2569 2.51 5 N 672 2.21 5 O 680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3952 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 3952 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 29, 'TRANS': 503} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 2.93, per 1000 atoms: 0.74 Number of scatterers: 3952 At special positions: 0 Unit cell: (104.86, 85.6, 64.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 680 8.00 N 672 7.00 C 2569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 541.0 milliseconds 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 2 sheets defined 83.3% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.732A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 42 removed outlier: 4.754A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.776A pdb=" N ARG A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 removed outlier: 3.550A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 Processing helix chain 'A' and resid 229 through 255 removed outlier: 3.829A pdb=" N PHE A 241 " --> pdb=" O ASN A 237 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.922A pdb=" N LEU A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.785A pdb=" N ASP A 313 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.742A pdb=" N LEU A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 368 removed outlier: 3.950A pdb=" N PHE A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.754A pdb=" N GLY A 375 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.751A pdb=" N THR A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 460 removed outlier: 3.889A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 490 removed outlier: 4.476A pdb=" N MET A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 495 through 513 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 526 through 538 removed outlier: 3.535A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 305 hydrogen bonds defined for protein. 882 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: 1.25 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1252 1.34 - 1.47: 984 1.47 - 1.59: 1761 1.59 - 1.71: 0 1.71 - 1.84: 50 Bond restraints: 4047 Sorted by residual: bond pdb=" C MET A 36 " pdb=" O MET A 36 " ideal model delta sigma weight residual 1.235 1.263 -0.028 1.38e-02 5.25e+03 4.04e+00 bond pdb=" CG PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.503 1.438 0.065 3.40e-02 8.65e+02 3.64e+00 bond pdb=" N PRO A 194 " pdb=" CA PRO A 194 " ideal model delta sigma weight residual 1.469 1.445 0.024 1.28e-02 6.10e+03 3.47e+00 bond pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.25e+00 bond pdb=" CB MET A 222 " pdb=" CG MET A 222 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 4042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 5385 3.17 - 6.34: 113 6.34 - 9.51: 17 9.51 - 12.68: 6 12.68 - 15.85: 5 Bond angle restraints: 5526 Sorted by residual: angle pdb=" CA PRO A 194 " pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 112.00 97.41 14.59 1.40e+00 5.10e-01 1.09e+02 angle pdb=" C ALA A 323 " pdb=" N MET A 324 " pdb=" CA MET A 324 " ideal model delta sigma weight residual 121.66 109.91 11.75 1.76e+00 3.23e-01 4.45e+01 angle pdb=" CB MET A 222 " pdb=" CG MET A 222 " pdb=" SD MET A 222 " ideal model delta sigma weight residual 112.70 97.37 15.33 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C THR A 518 " pdb=" N GLN A 519 " pdb=" CA GLN A 519 " ideal model delta sigma weight residual 125.66 134.53 -8.87 1.85e+00 2.92e-01 2.30e+01 angle pdb=" CB MET A 324 " pdb=" CG MET A 324 " pdb=" SD MET A 324 " ideal model delta sigma weight residual 112.70 125.54 -12.84 3.00e+00 1.11e-01 1.83e+01 ... (remaining 5521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 2132 17.27 - 34.55: 160 34.55 - 51.82: 51 51.82 - 69.09: 19 69.09 - 86.36: 4 Dihedral angle restraints: 2366 sinusoidal: 849 harmonic: 1517 Sorted by residual: dihedral pdb=" CA GLY A 375 " pdb=" C GLY A 375 " pdb=" N SER A 376 " pdb=" CA SER A 376 " ideal model delta harmonic sigma weight residual -180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 135.06 -42.06 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CD ARG A 487 " pdb=" NE ARG A 487 " pdb=" CZ ARG A 487 " pdb=" NH1 ARG A 487 " ideal model delta sinusoidal sigma weight residual 0.00 -28.91 28.91 1 1.00e+01 1.00e-02 1.20e+01 ... (remaining 2363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 459 0.051 - 0.101: 135 0.101 - 0.152: 45 0.152 - 0.202: 12 0.202 - 0.252: 4 Chirality restraints: 655 Sorted by residual: chirality pdb=" CA MET A 466 " pdb=" N MET A 466 " pdb=" C MET A 466 " pdb=" CB MET A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU A 13 " pdb=" CB LEU A 13 " pdb=" CD1 LEU A 13 " pdb=" CD2 LEU A 13 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ARG A 89 " pdb=" N ARG A 89 " pdb=" C ARG A 89 " pdb=" CB ARG A 89 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 652 not shown) Planarity restraints: 691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 193 " -0.143 5.00e-02 4.00e+02 2.05e-01 6.75e+01 pdb=" N PRO A 194 " 0.354 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 487 " -0.387 9.50e-02 1.11e+02 1.75e-01 2.36e+01 pdb=" NE ARG A 487 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 487 " -0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 487 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 487 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 291 " 0.311 9.50e-02 1.11e+02 1.40e-01 1.49e+01 pdb=" NE ARG A 291 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 291 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 291 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 291 " 0.001 2.00e-02 2.50e+03 ... (remaining 688 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 386 2.75 - 3.29: 4110 3.29 - 3.82: 6933 3.82 - 4.36: 7768 4.36 - 4.90: 13339 Nonbonded interactions: 32536 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" O PRO A 516 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 412 " pdb=" O GLY A 444 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 167 " pdb=" OD1 ASN A 216 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP A 257 " pdb=" OG1 THR A 259 " model vdw 2.291 3.040 nonbonded pdb=" O ALA A 359 " pdb=" OG1 THR A 363 " model vdw 2.297 3.040 ... (remaining 32531 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.210 Find NCS groups from input model: 0.040 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 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 : 0.005 0.070 4047 Z= 0.334 Angle : 1.210 15.847 5526 Z= 0.659 Chirality : 0.059 0.252 655 Planarity : 0.014 0.205 691 Dihedral : 15.276 86.364 1382 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.03 % Allowed : 21.83 % Favored : 76.14 % 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: 0.84 (0.34), residues: 529 helix: 1.01 (0.25), residues: 391 sheet: None (None), residues: 0 loop : -0.54 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.032 0.003 PHE A 208 TYR 0.030 0.008 TYR A 275 ARG 0.039 0.003 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.379 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.1039 time to fit residues: 73.4235 Evaluate side-chains 59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.210 Angle : 0.673 11.273 5526 Z= 0.327 Chirality : 0.041 0.134 655 Planarity : 0.006 0.095 691 Dihedral : 5.100 50.618 571 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.81 % Allowed : 20.81 % Favored : 75.38 % 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: 1.70 (0.38), residues: 529 helix: 1.64 (0.26), residues: 399 sheet: -1.07 (1.35), residues: 10 loop : -0.29 (0.62), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 294 HIS 0.004 0.001 HIS A 245 PHE 0.019 0.002 PHE A 208 TYR 0.017 0.003 TYR A 275 ARG 0.006 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.430 Fit side-chains REVERT: A 5 GLU cc_start: 0.6949 (mp0) cc_final: 0.6639 (mp0) REVERT: A 39 ASN cc_start: 0.8048 (t0) cc_final: 0.7821 (t0) REVERT: A 170 PHE cc_start: 0.8231 (m-80) cc_final: 0.8018 (m-80) REVERT: A 529 ASP cc_start: 0.6916 (t0) cc_final: 0.6704 (t0) outliers start: 15 outliers final: 4 residues processed: 80 average time/residue: 0.9709 time to fit residues: 80.9682 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.201 Angle : 0.652 9.732 5526 Z= 0.316 Chirality : 0.039 0.125 655 Planarity : 0.005 0.063 691 Dihedral : 4.893 57.110 569 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.05 % Allowed : 21.07 % Favored : 75.89 % 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: 2.01 (0.37), residues: 529 helix: 1.87 (0.26), residues: 387 sheet: -1.18 (1.36), residues: 10 loop : 0.05 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 294 HIS 0.005 0.001 HIS A 245 PHE 0.020 0.002 PHE A 208 TYR 0.019 0.003 TYR A 275 ARG 0.006 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.373 Fit side-chains REVERT: A 5 GLU cc_start: 0.7037 (mp0) cc_final: 0.6771 (mp0) REVERT: A 114 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6642 (pp20) REVERT: A 430 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6701 (mmm) outliers start: 12 outliers final: 5 residues processed: 75 average time/residue: 1.1523 time to fit residues: 89.6445 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 488 LEU 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: 0.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 51 optimal weight: 0.0170 chunk 45 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4047 Z= 0.163 Angle : 0.609 7.780 5526 Z= 0.292 Chirality : 0.037 0.116 655 Planarity : 0.004 0.045 691 Dihedral : 4.851 59.205 569 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.54 % Allowed : 22.34 % Favored : 75.13 % 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: 2.15 (0.37), residues: 529 helix: 1.96 (0.26), residues: 393 sheet: -1.13 (1.37), residues: 10 loop : 0.03 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 294 HIS 0.003 0.001 HIS A 245 PHE 0.020 0.002 PHE A 208 TYR 0.018 0.002 TYR A 275 ARG 0.009 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.394 Fit side-chains REVERT: A 228 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7802 (ttp80) REVERT: A 297 GLN cc_start: 0.7288 (tm-30) cc_final: 0.6798 (tp40) REVERT: A 300 TRP cc_start: 0.6859 (m-10) cc_final: 0.6571 (m-10) REVERT: A 430 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6565 (mmm) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.9917 time to fit residues: 70.3764 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.212 Angle : 0.623 7.725 5526 Z= 0.304 Chirality : 0.039 0.128 655 Planarity : 0.004 0.037 691 Dihedral : 4.796 56.866 569 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.31 % Allowed : 20.30 % Favored : 75.38 % 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: 1.97 (0.37), residues: 529 helix: 1.86 (0.26), residues: 395 sheet: -1.13 (1.40), residues: 10 loop : -0.20 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 294 HIS 0.005 0.001 HIS A 245 PHE 0.019 0.002 PHE A 208 TYR 0.020 0.002 TYR A 275 ARG 0.005 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.365 Fit side-chains REVERT: A 228 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.7897 (ttp80) REVERT: A 297 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6812 (tp40) REVERT: A 300 TRP cc_start: 0.7104 (m-10) cc_final: 0.6855 (m-10) REVERT: A 320 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6394 (tp) REVERT: A 369 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7539 (mt) REVERT: A 430 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6623 (mmm) outliers start: 17 outliers final: 8 residues processed: 80 average time/residue: 0.9404 time to fit residues: 78.4914 Evaluate side-chains 67 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4047 Z= 0.223 Angle : 0.628 8.500 5526 Z= 0.309 Chirality : 0.039 0.125 655 Planarity : 0.004 0.037 691 Dihedral : 4.784 54.932 569 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.30 % Allowed : 23.35 % Favored : 73.35 % 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: 1.89 (0.37), residues: 529 helix: 1.80 (0.26), residues: 393 sheet: -1.50 (1.44), residues: 10 loop : -0.11 (0.61), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 294 HIS 0.005 0.001 HIS A 245 PHE 0.020 0.002 PHE A 40 TYR 0.020 0.002 TYR A 275 ARG 0.004 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.404 Fit side-chains REVERT: A 228 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7994 (ttp80) REVERT: A 297 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6801 (tp40) REVERT: A 300 TRP cc_start: 0.7192 (m-10) cc_final: 0.6958 (m-10) REVERT: A 452 ILE cc_start: 0.8478 (tp) cc_final: 0.8274 (tp) outliers start: 13 outliers final: 5 residues processed: 75 average time/residue: 0.9660 time to fit residues: 75.4657 Evaluate side-chains 73 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4047 Z= 0.196 Angle : 0.631 9.291 5526 Z= 0.305 Chirality : 0.039 0.120 655 Planarity : 0.004 0.036 691 Dihedral : 4.711 50.877 569 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.28 % Allowed : 24.37 % Favored : 73.35 % 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: 1.98 (0.37), residues: 529 helix: 1.87 (0.26), residues: 393 sheet: -1.72 (1.49), residues: 10 loop : -0.11 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 495 HIS 0.004 0.001 HIS A 245 PHE 0.021 0.002 PHE A 40 TYR 0.019 0.002 TYR A 275 ARG 0.006 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 228 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.8018 (ttp80) REVERT: A 297 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6789 (tp40) REVERT: A 300 TRP cc_start: 0.7239 (m-10) cc_final: 0.7006 (m-10) REVERT: A 452 ILE cc_start: 0.8496 (tp) cc_final: 0.8275 (tp) REVERT: A 487 ARG cc_start: 0.6408 (tpp80) cc_final: 0.6066 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.9804 time to fit residues: 79.6374 Evaluate side-chains 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4047 Z= 0.190 Angle : 0.627 9.533 5526 Z= 0.301 Chirality : 0.039 0.120 655 Planarity : 0.004 0.035 691 Dihedral : 4.596 47.106 569 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.05 % Allowed : 24.62 % Favored : 72.34 % 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: 1.90 (0.37), residues: 529 helix: 1.81 (0.26), residues: 396 sheet: -1.63 (1.48), residues: 10 loop : -0.20 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 495 HIS 0.004 0.001 HIS A 245 PHE 0.021 0.002 PHE A 40 TYR 0.019 0.002 TYR A 275 ARG 0.005 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 88 CYS cc_start: 0.6229 (m) cc_final: 0.5864 (m) REVERT: A 228 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.7993 (ttp80) REVERT: A 278 TRP cc_start: 0.7287 (OUTLIER) cc_final: 0.6254 (t-100) REVERT: A 297 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6785 (tp40) REVERT: A 300 TRP cc_start: 0.7287 (m-10) cc_final: 0.7062 (m-10) REVERT: A 452 ILE cc_start: 0.8489 (tp) cc_final: 0.8269 (tp) REVERT: A 487 ARG cc_start: 0.6344 (tpp80) cc_final: 0.5993 (ttp-170) outliers start: 12 outliers final: 10 residues processed: 76 average time/residue: 0.9954 time to fit residues: 78.8553 Evaluate side-chains 75 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 278 TRP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4047 Z= 0.265 Angle : 0.681 11.276 5526 Z= 0.328 Chirality : 0.041 0.130 655 Planarity : 0.004 0.036 691 Dihedral : 4.668 44.869 569 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.79 % Allowed : 25.13 % Favored : 72.08 % 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: 1.63 (0.37), residues: 529 helix: 1.60 (0.26), residues: 396 sheet: -1.60 (1.55), residues: 10 loop : -0.25 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 495 HIS 0.005 0.001 HIS A 245 PHE 0.021 0.002 PHE A 40 TYR 0.020 0.002 TYR A 275 ARG 0.004 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 88 CYS cc_start: 0.6311 (m) cc_final: 0.5924 (m) REVERT: A 228 ARG cc_start: 0.8512 (ttp-110) cc_final: 0.8102 (ttp80) REVERT: A 297 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6760 (tp40) REVERT: A 300 TRP cc_start: 0.7403 (m-10) cc_final: 0.7199 (m-10) REVERT: A 487 ARG cc_start: 0.6410 (tpp80) cc_final: 0.6092 (ttp-170) REVERT: A 492 HIS cc_start: 0.6782 (t70) cc_final: 0.6182 (t-170) REVERT: A 495 TRP cc_start: 0.6474 (p-90) cc_final: 0.6026 (p90) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 1.0734 time to fit residues: 84.6990 Evaluate side-chains 75 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4047 Z= 0.195 Angle : 0.648 11.894 5526 Z= 0.312 Chirality : 0.039 0.123 655 Planarity : 0.004 0.035 691 Dihedral : 4.554 41.290 569 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 26.14 % Favored : 71.57 % 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: 1.78 (0.37), residues: 529 helix: 1.74 (0.26), residues: 396 sheet: -1.69 (1.60), residues: 10 loop : -0.30 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 495 HIS 0.002 0.001 HIS A 245 PHE 0.023 0.002 PHE A 40 TYR 0.019 0.002 TYR A 275 ARG 0.007 0.001 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1058 Ramachandran restraints generated. 529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 88 CYS cc_start: 0.6333 (m) cc_final: 0.5974 (m) REVERT: A 228 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8063 (ttp80) REVERT: A 297 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6748 (tp40) REVERT: A 364 PHE cc_start: 0.6969 (t80) cc_final: 0.6574 (t80) REVERT: A 487 ARG cc_start: 0.6380 (tpp80) cc_final: 0.6061 (ttp-170) REVERT: A 495 TRP cc_start: 0.6534 (p-90) cc_final: 0.6113 (p90) outliers start: 9 outliers final: 9 residues processed: 74 average time/residue: 0.9199 time to fit residues: 71.1548 Evaluate side-chains 74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 36 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123647 restraints weight = 4209.574| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.11 r_work: 0.3400 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4047 Z= 0.188 Angle : 0.640 11.429 5526 Z= 0.305 Chirality : 0.038 0.121 655 Planarity : 0.004 0.034 691 Dihedral : 4.403 35.036 569 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.78 % Allowed : 26.90 % Favored : 71.32 % 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: 1.85 (0.38), residues: 529 helix: 1.77 (0.26), residues: 397 sheet: -1.52 (1.66), residues: 10 loop : -0.25 (0.62), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 495 HIS 0.003 0.001 HIS A 245 PHE 0.021 0.002 PHE A 40 TYR 0.019 0.002 TYR A 275 ARG 0.008 0.001 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1997.37 seconds wall clock time: 36 minutes 15.35 seconds (2175.35 seconds total)