Starting phenix.real_space_refine on Tue Feb 13 06:09:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soc_25266/02_2024/7soc_25266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soc_25266/02_2024/7soc_25266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soc_25266/02_2024/7soc_25266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soc_25266/02_2024/7soc_25266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soc_25266/02_2024/7soc_25266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soc_25266/02_2024/7soc_25266.pdb" } resolution = 3.3 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= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2176 2.51 5 N 577 2.21 5 O 679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3448 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1589 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 2.81, per 1000 atoms: 0.81 Number of scatterers: 3448 At special positions: 0 Unit cell: (91.887, 78.399, 82.614, 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 16 16.00 O 679 8.00 N 577 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.10 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.07 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " BETA1-6 " NAG B 1 " - " FUC B 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 735.1 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 10.9% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.841A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.621A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.152A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.006A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.658A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.803A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 116 hydrogen bonds defined for protein. 261 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: 0.91 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 930 1.33 - 1.46: 914 1.46 - 1.58: 1671 1.58 - 1.71: 0 1.71 - 1.84: 19 Bond restraints: 3534 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.465 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N ASP H 115 " pdb=" CA ASP H 115 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.37e+00 ... (remaining 3529 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 104 106.88 - 113.67: 1872 113.67 - 120.45: 1368 120.45 - 127.24: 1433 127.24 - 134.02: 27 Bond angle restraints: 4804 Sorted by residual: angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 126.74 -7.18 1.02e+00 9.61e-01 4.95e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.89 126.97 -7.08 1.02e+00 9.61e-01 4.82e+01 angle pdb=" C LEU A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.85 126.82 -6.97 1.01e+00 9.80e-01 4.76e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.57 -7.01 1.02e+00 9.61e-01 4.72e+01 angle pdb=" C THR A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.78 126.73 -6.95 1.03e+00 9.43e-01 4.55e+01 ... (remaining 4799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 2076 21.66 - 43.32: 54 43.32 - 64.97: 12 64.97 - 86.63: 12 86.63 - 108.29: 4 Dihedral angle restraints: 2158 sinusoidal: 919 harmonic: 1239 Sorted by residual: dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.58 108.29 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.62 107.24 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C6 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O4 BMA B 3 " ideal model delta sinusoidal sigma weight residual -163.34 -61.42 -101.92 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 2155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 414 0.075 - 0.150: 95 0.150 - 0.225: 21 0.225 - 0.299: 3 0.299 - 0.374: 3 Chirality restraints: 536 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.16e+01 chirality pdb=" C1 MAN B 4 " pdb=" O3 BMA B 3 " pdb=" C2 MAN B 4 " pdb=" O5 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.40 2.46 -0.06 2.00e-02 2.50e+03 9.33e+00 ... (remaining 533 not shown) Planarity restraints: 614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 113 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C GLY H 113 " -0.051 2.00e-02 2.50e+03 pdb=" O GLY H 113 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE H 114 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.023 2.00e-02 2.50e+03 2.30e-02 6.62e+00 pdb=" CG ASN A 331 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 382 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C VAL A 382 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 382 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 383 " -0.012 2.00e-02 2.50e+03 ... (remaining 611 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 1858 3.00 - 3.48: 2935 3.48 - 3.95: 5779 3.95 - 4.43: 6532 4.43 - 4.90: 10740 Nonbonded interactions: 27844 Sorted by model distance: nonbonded pdb=" N ASP H 115 " pdb=" OD1 ASP H 115 " model vdw 2.526 2.520 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.528 2.520 nonbonded pdb=" N ASP A 428 " pdb=" OD1 ASP A 428 " model vdw 2.592 2.520 nonbonded pdb=" N ASP H 89 " pdb=" OD1 ASP H 89 " model vdw 2.598 2.520 nonbonded pdb=" N GLU L 80 " pdb=" O GLU L 80 " model vdw 2.607 2.496 ... (remaining 27839 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: 5.930 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: 27.760 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.062 3534 Z= 0.708 Angle : 1.221 7.554 4804 Z= 0.814 Chirality : 0.072 0.374 536 Planarity : 0.005 0.029 612 Dihedral : 13.133 108.287 1358 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.30 (0.39), residues: 427 helix: -4.85 (0.23), residues: 27 sheet: 0.86 (0.41), residues: 154 loop : 0.50 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP H 50 HIS 0.002 0.001 HIS L 92 PHE 0.032 0.003 PHE A 329 TYR 0.023 0.003 TYR A 495 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.389 Fit side-chains REVERT: A 340 GLU cc_start: 0.8715 (pt0) cc_final: 0.8477 (pt0) REVERT: A 378 LYS cc_start: 0.8603 (mttt) cc_final: 0.8141 (mtmt) REVERT: A 406 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 517 LEU cc_start: 0.6915 (tp) cc_final: 0.6336 (tp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2095 time to fit residues: 14.3988 Evaluate side-chains 35 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.8317 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3534 Z= 0.286 Angle : 0.542 5.510 4804 Z= 0.292 Chirality : 0.047 0.190 536 Planarity : 0.005 0.034 612 Dihedral : 10.484 86.694 617 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.65 % Allowed : 5.23 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.40), residues: 427 helix: -4.21 (0.52), residues: 27 sheet: 0.72 (0.40), residues: 158 loop : 0.60 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS L 92 PHE 0.020 0.002 PHE A 515 TYR 0.026 0.002 TYR A 495 ARG 0.003 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.409 Fit side-chains REVERT: A 340 GLU cc_start: 0.8802 (pt0) cc_final: 0.8582 (pt0) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 0.1051 time to fit residues: 5.7728 Evaluate side-chains 35 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 115 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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: 0.8387 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 3534 Z= 0.396 Angle : 0.590 7.468 4804 Z= 0.304 Chirality : 0.049 0.305 536 Planarity : 0.005 0.038 612 Dihedral : 9.417 77.668 617 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.20 % Allowed : 6.06 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.12 (0.40), residues: 427 helix: -3.97 (0.62), residues: 27 sheet: 0.53 (0.40), residues: 158 loop : 0.41 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.004 0.002 HIS L 92 PHE 0.013 0.002 PHE A 515 TYR 0.027 0.002 TYR A 495 ARG 0.003 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.352 Fit side-chains REVERT: A 378 LYS cc_start: 0.8604 (mttt) cc_final: 0.8011 (mtmt) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.0898 time to fit residues: 4.7198 Evaluate side-chains 34 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3534 Z= 0.295 Angle : 0.537 7.784 4804 Z= 0.273 Chirality : 0.049 0.399 536 Planarity : 0.005 0.040 612 Dihedral : 8.574 68.851 617 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.20 % Allowed : 6.61 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.00 (0.41), residues: 427 helix: -3.94 (0.66), residues: 27 sheet: 0.43 (0.41), residues: 158 loop : 0.32 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 PHE 0.008 0.001 PHE A 490 TYR 0.017 0.002 TYR A 495 ARG 0.001 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.345 Fit side-chains REVERT: A 378 LYS cc_start: 0.8597 (mttt) cc_final: 0.8066 (mtmt) REVERT: L 82 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7557 (pm20) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.1076 time to fit residues: 5.4236 Evaluate side-chains 36 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8382 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3534 Z= 0.287 Angle : 0.515 7.219 4804 Z= 0.261 Chirality : 0.047 0.330 536 Planarity : 0.004 0.038 612 Dihedral : 6.906 56.033 617 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 7.44 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.41), residues: 427 helix: -3.88 (0.59), residues: 33 sheet: 0.36 (0.41), residues: 158 loop : 0.24 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 PHE 0.007 0.001 PHE A 490 TYR 0.016 0.001 TYR A 495 ARG 0.001 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.380 Fit side-chains REVERT: A 378 LYS cc_start: 0.8521 (mttt) cc_final: 0.8040 (mtmt) REVERT: H 70 MET cc_start: 0.9291 (mtt) cc_final: 0.8694 (mtt) REVERT: L 82 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7628 (pm20) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.1099 time to fit residues: 5.2350 Evaluate side-chains 35 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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: 0.8369 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3534 Z= 0.225 Angle : 0.493 7.181 4804 Z= 0.253 Chirality : 0.048 0.469 536 Planarity : 0.004 0.037 612 Dihedral : 4.240 19.128 617 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.20 % Allowed : 7.71 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.11 (0.42), residues: 427 helix: -3.80 (0.63), residues: 33 sheet: 0.37 (0.41), residues: 158 loop : 0.34 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 PHE 0.006 0.001 PHE A 490 TYR 0.011 0.001 TYR A 495 ARG 0.001 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.355 Fit side-chains REVERT: A 378 LYS cc_start: 0.8444 (mttt) cc_final: 0.7963 (mtmt) REVERT: H 70 MET cc_start: 0.9276 (mtt) cc_final: 0.8696 (mtt) REVERT: L 82 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7596 (pm20) outliers start: 8 outliers final: 7 residues processed: 38 average time/residue: 0.0957 time to fit residues: 5.2277 Evaluate side-chains 38 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.8379 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3534 Z= 0.273 Angle : 0.503 7.521 4804 Z= 0.254 Chirality : 0.045 0.186 536 Planarity : 0.004 0.037 612 Dihedral : 4.883 50.434 617 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.93 % Allowed : 9.09 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.14 (0.42), residues: 427 helix: -3.77 (0.64), residues: 33 sheet: 0.34 (0.41), residues: 158 loop : 0.32 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.002 HIS L 92 PHE 0.007 0.001 PHE A 490 TYR 0.013 0.001 TYR A 495 ARG 0.002 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.389 Fit side-chains REVERT: A 378 LYS cc_start: 0.8429 (mttt) cc_final: 0.7929 (mtmt) REVERT: H 70 MET cc_start: 0.9261 (mtt) cc_final: 0.8621 (mtt) REVERT: L 82 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7601 (pm20) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.1108 time to fit residues: 5.3742 Evaluate side-chains 35 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8402 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 3534 Z= 0.347 Angle : 0.545 8.515 4804 Z= 0.273 Chirality : 0.046 0.152 536 Planarity : 0.004 0.039 612 Dihedral : 5.066 45.455 617 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.31 % Allowed : 8.26 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.23 (0.42), residues: 427 helix: -3.72 (0.67), residues: 33 sheet: 0.30 (0.42), residues: 157 loop : 0.22 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 PHE 0.008 0.001 PHE A 490 TYR 0.015 0.002 TYR A 495 ARG 0.001 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 27 time to evaluate : 0.386 Fit side-chains REVERT: A 378 LYS cc_start: 0.8448 (mttt) cc_final: 0.7921 (mtmt) REVERT: H 70 MET cc_start: 0.9263 (mtt) cc_final: 0.8649 (mtt) REVERT: L 82 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7623 (pm20) outliers start: 12 outliers final: 9 residues processed: 36 average time/residue: 0.1041 time to fit residues: 5.3988 Evaluate side-chains 37 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8396 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3534 Z= 0.306 Angle : 0.531 8.609 4804 Z= 0.264 Chirality : 0.044 0.140 536 Planarity : 0.004 0.037 612 Dihedral : 4.734 33.177 617 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 9.37 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.42), residues: 427 helix: -3.72 (0.66), residues: 33 sheet: 0.26 (0.41), residues: 158 loop : 0.22 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 PHE 0.007 0.001 PHE A 490 TYR 0.013 0.001 TYR A 495 ARG 0.001 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.380 Fit side-chains REVERT: A 378 LYS cc_start: 0.8440 (mttt) cc_final: 0.7904 (mtmt) REVERT: H 70 MET cc_start: 0.9251 (mtt) cc_final: 0.8648 (mtt) REVERT: L 82 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7591 (pm20) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.1079 time to fit residues: 5.1055 Evaluate side-chains 35 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8390 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3534 Z= 0.281 Angle : 0.513 8.099 4804 Z= 0.255 Chirality : 0.044 0.139 536 Planarity : 0.004 0.037 612 Dihedral : 4.752 36.742 617 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.48 % Allowed : 9.37 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.27 (0.42), residues: 427 helix: -3.66 (0.67), residues: 33 sheet: 0.23 (0.42), residues: 158 loop : 0.20 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.002 HIS L 92 PHE 0.006 0.001 PHE A 490 TYR 0.012 0.001 TYR A 495 ARG 0.002 0.000 ARG H 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.394 Fit side-chains REVERT: A 378 LYS cc_start: 0.8409 (mttt) cc_final: 0.7926 (mtmt) REVERT: A 466 ARG cc_start: 0.8818 (ttm110) cc_final: 0.8546 (ttp-170) REVERT: H 70 MET cc_start: 0.9247 (mtt) cc_final: 0.8634 (mtt) REVERT: L 82 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7599 (pm20) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.1272 time to fit residues: 6.2403 Evaluate side-chains 38 residues out of total 363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 29 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.0010 chunk 41 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.119907 restraints weight = 3838.227| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.74 r_work: 0.2778 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 0.049 3534 Z= 0.270 Angle : 0.514 8.291 4804 Z= 0.255 Chirality : 0.044 0.140 536 Planarity : 0.004 0.037 612 Dihedral : 4.844 37.128 617 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 9.64 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.24 (0.42), residues: 427 helix: -3.66 (0.66), residues: 33 sheet: 0.24 (0.42), residues: 158 loop : 0.23 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.002 HIS L 92 PHE 0.007 0.001 PHE A 490 TYR 0.012 0.001 TYR A 495 ARG 0.002 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.17 seconds wall clock time: 28 minutes 51.05 seconds (1731.05 seconds total)