Starting phenix.real_space_refine on Fri Apr 5 16:14:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzu_36753/04_2024/8jzu_36753.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzu_36753/04_2024/8jzu_36753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzu_36753/04_2024/8jzu_36753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzu_36753/04_2024/8jzu_36753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzu_36753/04_2024/8jzu_36753.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jzu_36753/04_2024/8jzu_36753.pdb" } resolution = 3.05 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= -0.002 sd= 0.049 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 22 5.16 5 C 2474 2.51 5 N 599 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3741 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3620 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 107 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.28, per 1000 atoms: 0.88 Number of scatterers: 3741 At special positions: 0 Unit cell: (80.1135, 67.464, 73.3671, 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 22 16.00 O 646 8.00 N 599 7.00 C 2474 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 436 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 884.0 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 80.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 33 through 57 removed outlier: 4.103A pdb=" N ALA A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 99 removed outlier: 4.196A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix removed outlier: 3.637A pdb=" N ARG A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 125 Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.109A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 184 removed outlier: 3.580A pdb=" N LEU A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.777A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 4.162A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 243 removed outlier: 3.727A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.399A pdb=" N ASP A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 337 Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 367 through 396 Proline residue: A 382 - end of helix removed outlier: 4.852A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 430 Processing helix chain 'A' and resid 450 through 453 removed outlier: 3.665A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.577A pdb=" N TYR A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 511 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.901A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 9 through 13 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 removed outlier: 4.083A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 822 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: 1.03 Time building geometry restraints manager: 1.79 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: 1121 1.34 - 1.46: 598 1.46 - 1.57: 2078 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3831 Sorted by residual: bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.427 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" CB ASN A 203 " pdb=" CG ASN A 203 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" C6 NAG A 601 " pdb=" O6 NAG A 601 " ideal model delta sigma weight residual 1.408 1.432 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 NAG A 601 " pdb=" O4 NAG A 601 " ideal model delta sigma weight residual 1.409 1.430 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" CG1 ILE A 466 " pdb=" CD1 ILE A 466 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.04e+00 ... (remaining 3826 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.69: 106 106.69 - 113.52: 2120 113.52 - 120.34: 1452 120.34 - 127.17: 1482 127.17 - 133.99: 44 Bond angle restraints: 5204 Sorted by residual: angle pdb=" N GLY A 64 " pdb=" CA GLY A 64 " pdb=" C GLY A 64 " ideal model delta sigma weight residual 111.20 115.12 -3.92 1.39e+00 5.18e-01 7.97e+00 angle pdb=" CA TYR A 199 " pdb=" CB TYR A 199 " pdb=" CG TYR A 199 " ideal model delta sigma weight residual 113.90 118.35 -4.45 1.80e+00 3.09e-01 6.11e+00 angle pdb=" N VAL A 322 " pdb=" CA VAL A 322 " pdb=" C VAL A 322 " ideal model delta sigma weight residual 108.88 114.19 -5.31 2.16e+00 2.14e-01 6.05e+00 angle pdb=" C LEU A 379 " pdb=" N LEU A 380 " pdb=" CA LEU A 380 " ideal model delta sigma weight residual 122.36 118.16 4.20 1.72e+00 3.38e-01 5.96e+00 angle pdb=" C GLN A 485 " pdb=" N SER A 486 " pdb=" CA SER A 486 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.63e+00 ... (remaining 5199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 2005 17.22 - 34.44: 186 34.44 - 51.65: 35 51.65 - 68.87: 4 68.87 - 86.09: 2 Dihedral angle restraints: 2232 sinusoidal: 842 harmonic: 1390 Sorted by residual: dihedral pdb=" CG ARG A 192 " pdb=" CD ARG A 192 " pdb=" NE ARG A 192 " pdb=" CZ ARG A 192 " ideal model delta sinusoidal sigma weight residual 180.00 135.39 44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU B 4 " pdb=" CG GLU B 4 " pdb=" CD GLU B 4 " pdb=" OE1 GLU B 4 " ideal model delta sinusoidal sigma weight residual 0.00 -86.09 86.09 1 3.00e+01 1.11e-03 9.94e+00 dihedral pdb=" CG LYS A 403 " pdb=" CD LYS A 403 " pdb=" CE LYS A 403 " pdb=" NZ LYS A 403 " ideal model delta sinusoidal sigma weight residual -180.00 -127.04 -52.96 3 1.50e+01 4.44e-03 9.16e+00 ... (remaining 2229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 412 0.034 - 0.068: 140 0.068 - 0.102: 42 0.102 - 0.136: 12 0.136 - 0.169: 4 Chirality restraints: 610 Sorted by residual: chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 436 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CB VAL A 183 " pdb=" CA VAL A 183 " pdb=" CG1 VAL A 183 " pdb=" CG2 VAL A 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 607 not shown) Planarity restraints: 639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 436 " 0.019 2.00e-02 2.50e+03 2.28e-02 6.50e+00 pdb=" CG ASN A 436 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A 436 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 436 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 199 " -0.011 2.00e-02 2.50e+03 1.42e-02 4.04e+00 pdb=" CG TYR A 199 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 199 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 199 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 199 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 199 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 199 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 199 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 456 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.026 5.00e-02 4.00e+02 ... (remaining 636 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 416 2.74 - 3.28: 3819 3.28 - 3.82: 6363 3.82 - 4.36: 7015 4.36 - 4.90: 12664 Nonbonded interactions: 30277 Sorted by model distance: nonbonded pdb=" O MET A 117 " pdb=" OG1 THR A 230 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR A 86 " pdb=" N MET B 1 " model vdw 2.266 2.520 nonbonded pdb=" OD1 ASN A 428 " pdb=" NZ LYS A 431 " model vdw 2.279 2.520 nonbonded pdb=" O LEU A 122 " pdb=" OG1 THR A 128 " model vdw 2.306 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.347 2.440 ... (remaining 30272 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: 2.180 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: 0.000 Extract box with map and model: 4.690 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.130 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3831 Z= 0.230 Angle : 0.587 6.119 5204 Z= 0.299 Chirality : 0.040 0.169 610 Planarity : 0.004 0.046 638 Dihedral : 13.672 86.091 1339 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 1.94 (0.40), residues: 476 helix: 2.08 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -1.39 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 453 HIS 0.003 0.001 HIS A 348 PHE 0.016 0.001 PHE A 195 TYR 0.035 0.002 TYR A 199 ARG 0.001 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.396 Fit side-chains REVERT: A 172 LYS cc_start: 0.7455 (ttpp) cc_final: 0.6745 (ttmt) REVERT: A 316 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7700 (mmtt) REVERT: A 321 ILE cc_start: 0.8318 (mt) cc_final: 0.8011 (mt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2006 time to fit residues: 31.3076 Evaluate side-chains 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 GLN A 337 GLN A 345 GLN A 454 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3831 Z= 0.221 Angle : 0.574 6.072 5204 Z= 0.290 Chirality : 0.039 0.164 610 Planarity : 0.004 0.049 638 Dihedral : 4.024 17.324 537 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.80 % Allowed : 11.86 % Favored : 86.34 % 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: 1.89 (0.39), residues: 476 helix: 2.02 (0.27), residues: 365 sheet: None (None), residues: 0 loop : -1.42 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.009 0.002 HIS A 303 PHE 0.012 0.002 PHE A 198 TYR 0.020 0.002 TYR A 113 ARG 0.006 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.420 Fit side-chains REVERT: A 172 LYS cc_start: 0.7755 (ttpp) cc_final: 0.6869 (ttmm) REVERT: A 321 ILE cc_start: 0.8370 (mt) cc_final: 0.8086 (mt) outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.1285 time to fit residues: 15.1306 Evaluate side-chains 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3831 Z= 0.226 Angle : 0.544 6.047 5204 Z= 0.272 Chirality : 0.038 0.160 610 Planarity : 0.004 0.049 638 Dihedral : 3.917 18.947 537 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.35 % Allowed : 16.49 % Favored : 80.15 % 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: 1.61 (0.39), residues: 476 helix: 1.80 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.55 (0.56), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 368 HIS 0.005 0.001 HIS A 348 PHE 0.020 0.002 PHE A 198 TYR 0.028 0.003 TYR A 342 ARG 0.005 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 465 GLU cc_start: 0.7361 (tt0) cc_final: 0.6824 (tt0) outliers start: 13 outliers final: 6 residues processed: 87 average time/residue: 0.1207 time to fit residues: 14.2399 Evaluate side-chains 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.0670 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 174 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3831 Z= 0.214 Angle : 0.533 6.250 5204 Z= 0.266 Chirality : 0.037 0.153 610 Planarity : 0.004 0.047 638 Dihedral : 3.862 18.805 537 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.84 % Allowed : 18.56 % Favored : 78.61 % 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: 1.61 (0.39), residues: 476 helix: 1.79 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.55 (0.56), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.021 0.002 PHE A 194 TYR 0.021 0.002 TYR A 342 ARG 0.003 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 400 SER cc_start: 0.7528 (p) cc_final: 0.7101 (t) REVERT: A 465 GLU cc_start: 0.7179 (tt0) cc_final: 0.6872 (tt0) outliers start: 11 outliers final: 6 residues processed: 77 average time/residue: 0.1112 time to fit residues: 11.5910 Evaluate side-chains 72 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3831 Z= 0.215 Angle : 0.531 6.325 5204 Z= 0.263 Chirality : 0.037 0.144 610 Planarity : 0.004 0.048 638 Dihedral : 3.845 17.697 537 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.58 % Allowed : 18.30 % Favored : 79.12 % 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: 1.61 (0.38), residues: 476 helix: 1.81 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.61 (0.54), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 453 HIS 0.003 0.001 HIS A 348 PHE 0.017 0.001 PHE A 194 TYR 0.022 0.002 TYR A 342 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 400 SER cc_start: 0.7497 (p) cc_final: 0.7098 (t) REVERT: A 465 GLU cc_start: 0.7286 (tt0) cc_final: 0.7036 (tt0) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.1200 time to fit residues: 12.3615 Evaluate side-chains 76 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3831 Z= 0.230 Angle : 0.536 6.021 5204 Z= 0.270 Chirality : 0.037 0.143 610 Planarity : 0.004 0.047 638 Dihedral : 3.880 20.419 537 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 19.33 % Favored : 77.32 % 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: 1.53 (0.38), residues: 476 helix: 1.72 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.53 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.028 0.001 PHE A 194 TYR 0.019 0.002 TYR B 6 ARG 0.002 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8056 (tt) REVERT: A 321 ILE cc_start: 0.8748 (mp) cc_final: 0.8529 (mp) REVERT: A 400 SER cc_start: 0.7496 (p) cc_final: 0.7095 (t) REVERT: A 465 GLU cc_start: 0.7235 (tt0) cc_final: 0.7020 (tt0) outliers start: 13 outliers final: 8 residues processed: 78 average time/residue: 0.1164 time to fit residues: 12.1514 Evaluate side-chains 79 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3831 Z= 0.224 Angle : 0.543 6.361 5204 Z= 0.272 Chirality : 0.037 0.142 610 Planarity : 0.004 0.047 638 Dihedral : 3.835 15.634 537 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 18.04 % Favored : 78.61 % 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: 1.62 (0.38), residues: 476 helix: 1.77 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.44 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.027 0.001 PHE A 194 TYR 0.021 0.002 TYR B 6 ARG 0.002 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8021 (tt) REVERT: A 320 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7709 (mttm) REVERT: A 400 SER cc_start: 0.7474 (p) cc_final: 0.7090 (t) REVERT: A 465 GLU cc_start: 0.7242 (tt0) cc_final: 0.6893 (tt0) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1222 time to fit residues: 13.3914 Evaluate side-chains 83 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3831 Z= 0.229 Angle : 0.553 6.180 5204 Z= 0.278 Chirality : 0.037 0.140 610 Planarity : 0.004 0.047 638 Dihedral : 3.882 20.686 537 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.58 % Allowed : 19.33 % Favored : 78.09 % 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: 1.57 (0.38), residues: 476 helix: 1.74 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.48 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.024 0.001 PHE A 194 TYR 0.018 0.002 TYR B 6 ARG 0.005 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8009 (tt) REVERT: A 320 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7699 (mtpp) REVERT: A 321 ILE cc_start: 0.8746 (mp) cc_final: 0.8546 (mp) REVERT: A 400 SER cc_start: 0.7467 (p) cc_final: 0.7097 (t) REVERT: A 465 GLU cc_start: 0.7213 (tt0) cc_final: 0.6936 (tt0) outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.1208 time to fit residues: 12.6068 Evaluate side-chains 79 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3831 Z= 0.211 Angle : 0.556 6.904 5204 Z= 0.277 Chirality : 0.037 0.140 610 Planarity : 0.004 0.047 638 Dihedral : 3.807 15.064 537 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.06 % Allowed : 19.85 % Favored : 78.09 % 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: 1.65 (0.38), residues: 476 helix: 1.82 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.016 0.001 PHE A 198 TYR 0.018 0.002 TYR B 6 ARG 0.002 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8091 (tt) REVERT: A 320 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7625 (mtpp) REVERT: A 321 ILE cc_start: 0.8771 (mp) cc_final: 0.8539 (mp) REVERT: A 400 SER cc_start: 0.7527 (p) cc_final: 0.7136 (t) REVERT: A 465 GLU cc_start: 0.7207 (tt0) cc_final: 0.6898 (tt0) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.1285 time to fit residues: 13.8900 Evaluate side-chains 79 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 11 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3831 Z= 0.201 Angle : 0.567 11.334 5204 Z= 0.279 Chirality : 0.037 0.141 610 Planarity : 0.004 0.046 638 Dihedral : 3.812 20.312 537 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.06 % Allowed : 19.33 % Favored : 78.61 % 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: 1.68 (0.38), residues: 476 helix: 1.84 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.53 (0.54), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.012 0.001 PHE A 195 TYR 0.017 0.002 TYR B 6 ARG 0.002 0.000 ARG A 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8060 (tt) REVERT: A 321 ILE cc_start: 0.8770 (mp) cc_final: 0.8533 (mp) REVERT: A 400 SER cc_start: 0.7548 (p) cc_final: 0.7153 (t) REVERT: A 465 GLU cc_start: 0.7222 (tt0) cc_final: 0.6919 (tt0) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.1244 time to fit residues: 12.9354 Evaluate side-chains 80 residues out of total 391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 554 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.186067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.161421 restraints weight = 4650.919| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.92 r_work: 0.3877 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3831 Z= 0.211 Angle : 0.597 15.099 5204 Z= 0.287 Chirality : 0.038 0.164 610 Planarity : 0.004 0.047 638 Dihedral : 3.775 15.289 537 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.32 % Allowed : 19.07 % Favored : 78.61 % 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: 1.66 (0.38), residues: 476 helix: 1.82 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS A 348 PHE 0.016 0.001 PHE A 198 TYR 0.017 0.002 TYR B 6 ARG 0.001 0.000 ARG A 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1240.53 seconds wall clock time: 23 minutes 12.73 seconds (1392.73 seconds total)