Starting phenix.real_space_refine on Wed Mar 5 21:41:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soc_25266/03_2025/7soc_25266.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soc_25266/03_2025/7soc_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/cci-nas-00/data/ceres_data/7soc_25266/03_2025/7soc_25266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soc_25266/03_2025/7soc_25266.map" model { file = "/net/cci-nas-00/data/ceres_data/7soc_25266/03_2025/7soc_25266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soc_25266/03_2025/7soc_25266.cif" } 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. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.73, per 1000 atoms: 1.37 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 1.07 Conformation dependent library (CDL) restraints added in 452.9 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: 0.50 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: 0.96 Time building geometry restraints manager: 1.24 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: 0.00 - 1.51: 4088 1.51 - 3.02: 584 3.02 - 4.53: 79 4.53 - 6.04: 34 6.04 - 7.55: 19 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 3.120 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.528 3.120 nonbonded pdb=" N ASP A 428 " pdb=" OD1 ASP A 428 " model vdw 2.592 3.120 nonbonded pdb=" N ASP H 89 " pdb=" OD1 ASP H 89 " model vdw 2.598 3.120 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 Time spend for trying shortcut: 0.00 ========== 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: 8.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.580 Find NCS groups from input model: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.345 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: 0.1773 time to fit residues: 12.0149 Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 0.4980 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.3130 r_free = 0.3130 target = 0.111796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.097944 restraints weight = 4105.795| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.26 r_work: 0.2849 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3534 Z= 0.217 Angle : 0.515 5.245 4804 Z= 0.279 Chirality : 0.046 0.191 536 Planarity : 0.004 0.031 612 Dihedral : 10.400 85.676 617 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.38 % Allowed : 4.96 % Favored : 93.66 % 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: 0.41 (0.40), residues: 427 helix: -4.30 (0.47), residues: 27 sheet: 0.73 (0.40), residues: 159 loop : 0.68 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS L 92 PHE 0.019 0.002 PHE A 515 TYR 0.019 0.001 TYR A 495 ARG 0.003 0.000 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 to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.373 Fit side-chains REVERT: A 340 GLU cc_start: 0.8823 (pt0) cc_final: 0.8596 (pt0) REVERT: A 378 LYS cc_start: 0.8779 (mttt) cc_final: 0.8037 (mtmt) REVERT: H 102 ARG cc_start: 0.9310 (ttm-80) cc_final: 0.8931 (ttm-80) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.1337 time to fit residues: 7.2186 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.108782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.093102 restraints weight = 4140.198| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.46 r_work: 0.2774 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 3534 Z= 0.388 Angle : 0.579 6.394 4804 Z= 0.305 Chirality : 0.048 0.218 536 Planarity : 0.005 0.036 612 Dihedral : 9.392 76.634 617 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 6.61 % 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: 0.15 (0.40), residues: 427 helix: -4.08 (0.58), residues: 27 sheet: 0.52 (0.40), residues: 159 loop : 0.46 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.004 0.001 HIS L 92 PHE 0.014 0.002 PHE A 429 TYR 0.025 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 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.380 Fit side-chains REVERT: A 378 LYS cc_start: 0.8854 (mttt) cc_final: 0.8094 (mtmt) REVERT: L 82 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7977 (pm20) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.0997 time to fit residues: 5.1610 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 7 SER Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.092966 restraints weight = 4185.007| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.49 r_work: 0.2770 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3534 Z= 0.326 Angle : 0.547 6.169 4804 Z= 0.280 Chirality : 0.048 0.320 536 Planarity : 0.005 0.039 612 Dihedral : 8.482 67.004 617 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -0.01 (0.41), residues: 427 helix: -3.99 (0.64), residues: 27 sheet: 0.46 (0.41), residues: 157 loop : 0.30 (0.41), residues: 243 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 0.010 0.001 PHE L 84 TYR 0.018 0.002 TYR A 495 ARG 0.002 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 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.330 Fit side-chains REVERT: A 378 LYS cc_start: 0.8839 (mttt) cc_final: 0.8145 (mtmt) REVERT: L 82 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7820 (pm20) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.0978 time to fit residues: 5.1890 Evaluate side-chains 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3087 r_free = 0.3087 target = 0.108677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.093852 restraints weight = 4240.704| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.40 r_work: 0.2784 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3534 Z= 0.319 Angle : 0.551 6.755 4804 Z= 0.282 Chirality : 0.050 0.432 536 Planarity : 0.005 0.040 612 Dihedral : 7.756 57.994 617 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.65 % Allowed : 8.26 % 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: -0.14 (0.41), residues: 427 helix: -3.89 (0.71), residues: 27 sheet: 0.32 (0.41), residues: 157 loop : 0.21 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 PHE 0.009 0.001 PHE L 84 TYR 0.017 0.002 TYR A 495 ARG 0.002 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 33 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.370 Fit side-chains REVERT: A 378 LYS cc_start: 0.8810 (mttt) cc_final: 0.8135 (mtmt) REVERT: H 70 MET cc_start: 0.9334 (mtt) cc_final: 0.8728 (mtt) REVERT: L 82 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7820 (pm20) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.1093 time to fit residues: 5.0208 Evaluate side-chains 32 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 38 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.138376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.119273 restraints weight = 3934.992| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.83 r_work: 0.2764 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2762 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= 0.287 Angle : 0.528 6.686 4804 Z= 0.267 Chirality : 0.045 0.143 536 Planarity : 0.004 0.038 612 Dihedral : 5.975 52.862 617 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.65 % Allowed : 9.09 % Favored : 89.26 % 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 (0.42), residues: 427 helix: -3.88 (0.62), residues: 33 sheet: 0.27 (0.41), residues: 157 loop : 0.18 (0.43), residues: 237 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 0.008 0.001 PHE L 84 TYR 0.015 0.001 TYR A 495 ARG 0.002 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 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.314 Fit side-chains REVERT: A 378 LYS cc_start: 0.8837 (mttt) cc_final: 0.8041 (mtmt) REVERT: H 70 MET cc_start: 0.9361 (mtt) cc_final: 0.8747 (mtt) outliers start: 6 outliers final: 5 residues processed: 34 average time/residue: 0.0904 time to fit residues: 4.4812 Evaluate side-chains 33 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.138150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.119432 restraints weight = 3868.449| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.78 r_work: 0.2775 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2868 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= 0.277 Angle : 0.522 7.918 4804 Z= 0.264 Chirality : 0.045 0.179 536 Planarity : 0.004 0.038 612 Dihedral : 4.589 32.994 617 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.93 % Allowed : 8.54 % Favored : 89.53 % 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: -0.28 (0.42), residues: 427 helix: -3.84 (0.63), residues: 33 sheet: 0.25 (0.41), residues: 157 loop : 0.21 (0.43), residues: 237 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 L 84 TYR 0.014 0.001 TYR A 495 ARG 0.002 0.000 ARG H 67 *********************** 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 to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.382 Fit side-chains REVERT: A 378 LYS cc_start: 0.8829 (mttt) cc_final: 0.8040 (mtmt) REVERT: H 43 GLN cc_start: 0.8650 (mm110) cc_final: 0.8353 (mp10) REVERT: H 70 MET cc_start: 0.9362 (mtt) cc_final: 0.8759 (mtt) REVERT: L 82 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.7909 (pm20) outliers start: 7 outliers final: 6 residues processed: 35 average time/residue: 0.1050 time to fit residues: 5.3105 Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.137286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.118645 restraints weight = 3918.340| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.77 r_work: 0.2761 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 3534 Z= 0.332 Angle : 0.540 7.002 4804 Z= 0.273 Chirality : 0.046 0.155 536 Planarity : 0.004 0.039 612 Dihedral : 4.933 37.103 617 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 8.26 % Favored : 89.53 % 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: -0.31 (0.42), residues: 427 helix: -3.79 (0.64), residues: 33 sheet: 0.24 (0.42), residues: 157 loop : 0.17 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 PHE 0.008 0.001 PHE L 84 TYR 0.016 0.002 TYR A 495 ARG 0.002 0.000 ARG H 67 *********************** 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 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.336 Fit side-chains REVERT: A 378 LYS cc_start: 0.8828 (mttt) cc_final: 0.8054 (mtmt) REVERT: H 70 MET cc_start: 0.9361 (mtt) cc_final: 0.8678 (mtt) REVERT: L 82 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7956 (pm20) outliers start: 8 outliers final: 7 residues processed: 32 average time/residue: 0.1001 time to fit residues: 4.6289 Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR 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 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 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 29 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.139128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.120671 restraints weight = 3797.566| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.75 r_work: 0.2822 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3534 Z= 0.227 Angle : 0.496 6.436 4804 Z= 0.250 Chirality : 0.044 0.141 536 Planarity : 0.004 0.036 612 Dihedral : 4.775 36.325 617 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.65 % Allowed : 8.82 % Favored : 89.53 % 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: -0.07 (0.43), residues: 427 helix: -3.51 (0.75), residues: 27 sheet: 0.28 (0.42), residues: 157 loop : 0.29 (0.44), residues: 243 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 H 29 TYR 0.011 0.001 TYR A 369 ARG 0.002 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 to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.517 Fit side-chains REVERT: A 378 LYS cc_start: 0.8829 (mttt) cc_final: 0.8044 (mtmt) REVERT: H 43 GLN cc_start: 0.8575 (mp10) cc_final: 0.8193 (mp10) REVERT: H 70 MET cc_start: 0.9345 (mtt) cc_final: 0.8599 (mtt) REVERT: L 82 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7955 (pm20) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.1084 time to fit residues: 5.2923 Evaluate side-chains 33 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER 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 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 41 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.138055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.119551 restraints weight = 3863.963| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.75 r_work: 0.2777 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3534 Z= 0.272 Angle : 0.513 6.746 4804 Z= 0.258 Chirality : 0.044 0.141 536 Planarity : 0.004 0.038 612 Dihedral : 4.851 36.513 617 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.38 % Allowed : 8.82 % Favored : 89.81 % 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: -0.09 (0.43), residues: 427 helix: -3.47 (0.77), residues: 27 sheet: 0.24 (0.42), residues: 157 loop : 0.29 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.002 HIS L 92 PHE 0.007 0.001 PHE H 29 TYR 0.013 0.001 TYR A 495 ARG 0.002 0.000 ARG H 67 ********************** 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 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.375 Fit side-chains REVERT: A 378 LYS cc_start: 0.8774 (mttt) cc_final: 0.8046 (mtmt) REVERT: H 43 GLN cc_start: 0.8556 (mp10) cc_final: 0.8204 (mp10) REVERT: H 70 MET cc_start: 0.9340 (mtt) cc_final: 0.8699 (mtt) REVERT: L 82 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7924 (pm20) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.1043 time to fit residues: 4.9707 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER 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 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.110727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.094056 restraints weight = 4126.748| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.58 r_work: 0.2787 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3534 Z= 0.285 Angle : 0.524 7.395 4804 Z= 0.264 Chirality : 0.044 0.141 536 Planarity : 0.004 0.038 612 Dihedral : 4.913 36.955 617 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.38 % Allowed : 9.09 % Favored : 89.53 % 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: -0.13 (0.43), residues: 427 helix: -3.41 (0.80), residues: 27 sheet: 0.21 (0.42), residues: 157 loop : 0.25 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 PHE 0.007 0.001 PHE H 29 TYR 0.013 0.001 TYR A 495 ARG 0.003 0.000 ARG H 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2407.91 seconds wall clock time: 42 minutes 4.18 seconds (2524.18 seconds total)