Starting phenix.real_space_refine on Tue Feb 11 02:32:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7soc_25266/02_2025/7soc_25266.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soc_25266/02_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_25266/02_2025/7soc_25266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soc_25266/02_2025/7soc_25266.map" model { file = "/net/cci-nas-00/data/ceres_data/7soc_25266/02_2025/7soc_25266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soc_25266/02_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-5592/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: 5.50, per 1000 atoms: 1.60 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: 1.11 Conformation dependent library (CDL) restraints added in 429.9 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: 0.47 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: 1.27 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: 8.450 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- 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 : 0.368 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: 0.1686 time to fit residues: 11.4123 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 : 0.307 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3128 r_free = 0.3128 target = 0.111740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.097740 restraints weight = 4110.599| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.30 r_work: 0.2844 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1461 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 5.242 4804 Z= 0.279 Chirality : 0.046 0.191 536 Planarity : 0.004 0.032 612 Dihedral : 10.401 85.686 617 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 : 0.401 Fit side-chains REVERT: A 340 GLU cc_start: 0.8822 (pt0) cc_final: 0.8589 (pt0) REVERT: A 378 LYS cc_start: 0.8786 (mttt) cc_final: 0.8019 (mtmt) REVERT: A 471 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7997 (mt-10) REVERT: H 102 ARG cc_start: 0.9303 (ttm-80) cc_final: 0.8920 (ttm-80) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.1333 time to fit residues: 7.0747 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 : 0.366 ------------------------------------------------------------------------------- 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: 0.7980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.108517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.092842 restraints weight = 4138.194| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.45 r_work: 0.2773 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 3534 Z= 0.423 Angle : 0.589 6.509 4804 Z= 0.309 Chirality : 0.049 0.218 536 Planarity : 0.005 0.036 612 Dihedral : 9.566 78.346 617 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 6.34 % Favored : 92.01 % 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 (0.40), residues: 427 helix: -4.06 (0.59), residues: 27 sheet: 0.51 (0.40), residues: 159 loop : 0.45 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.004 0.002 HIS L 92 PHE 0.017 0.002 PHE A 429 TYR 0.028 0.002 TYR A 495 ARG 0.004 0.001 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 : 0.345 Fit side-chains REVERT: A 378 LYS cc_start: 0.8854 (mttt) cc_final: 0.8100 (mtmt) REVERT: A 471 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8200 (mt-10) REVERT: L 82 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7987 (pm20) outliers start: 6 outliers final: 5 residues processed: 36 average time/residue: 0.0996 time to fit residues: 5.1306 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 : 0.392 ------------------------------------------------------------------------------- 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: 0.6980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3111 r_free = 0.3111 target = 0.110254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.094408 restraints weight = 4163.525| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.46 r_work: 0.2796 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3534 Z= 0.244 Angle : 0.508 5.973 4804 Z= 0.261 Chirality : 0.047 0.340 536 Planarity : 0.004 0.038 612 Dihedral : 8.610 69.333 617 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.83 % Allowed : 7.71 % Favored : 91.46 % 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 (0.41), residues: 427 helix: -4.00 (0.64), residues: 27 sheet: 0.49 (0.41), residues: 158 loop : 0.41 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 92 PHE 0.007 0.001 PHE H 29 TYR 0.015 0.001 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 32 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.372 Fit side-chains REVERT: A 378 LYS cc_start: 0.8851 (mttt) cc_final: 0.8148 (mtmt) REVERT: A 471 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8221 (mt-10) REVERT: L 82 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8034 (pm20) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.1108 time to fit residues: 4.7654 Evaluate side-chains 31 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR 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: 1.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3107 r_free = 0.3107 target = 0.110108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.092839 restraints weight = 4123.886| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.62 r_work: 0.2770 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 3534 Z= 0.379 Angle : 0.566 7.012 4804 Z= 0.290 Chirality : 0.048 0.270 536 Planarity : 0.005 0.041 612 Dihedral : 6.969 52.928 617 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.48 % Allowed : 6.61 % Favored : 90.91 % 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: -0.37 (0.41), residues: 427 helix: -3.92 (0.59), residues: 33 sheet: 0.20 (0.41), residues: 158 loop : 0.14 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.005 0.002 HIS L 92 PHE 0.011 0.002 PHE L 84 TYR 0.019 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 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.369 Fit side-chains REVERT: A 378 LYS cc_start: 0.8852 (mttt) cc_final: 0.8074 (mtmt) REVERT: A 471 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8203 (mt-10) REVERT: H 70 MET cc_start: 0.9374 (mtt) cc_final: 0.8744 (mtt) outliers start: 9 outliers final: 9 residues processed: 32 average time/residue: 0.1134 time to fit residues: 5.2935 Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3124 r_free = 0.3124 target = 0.111487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.094300 restraints weight = 4131.166| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.62 r_work: 0.2786 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3534 Z= 0.248 Angle : 0.511 6.534 4804 Z= 0.265 Chirality : 0.047 0.399 536 Planarity : 0.004 0.038 612 Dihedral : 4.461 19.167 617 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.38 % Allowed : 8.26 % 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: -0.26 (0.42), residues: 427 helix: -3.89 (0.61), residues: 33 sheet: 0.25 (0.41), residues: 157 loop : 0.24 (0.43), residues: 237 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 L 84 TYR 0.012 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 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.348 Fit side-chains REVERT: A 378 LYS cc_start: 0.8821 (mttt) cc_final: 0.8052 (mtmt) REVERT: A 471 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8225 (mt-10) REVERT: H 43 GLN cc_start: 0.8595 (mm110) cc_final: 0.8281 (mp10) REVERT: H 70 MET cc_start: 0.9344 (mtt) cc_final: 0.8705 (mtt) REVERT: L 82 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7868 (pm20) outliers start: 5 outliers final: 4 residues processed: 33 average time/residue: 0.1107 time to fit residues: 5.1635 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 : 0.366 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.0470 chunk 25 optimal weight: 0.0170 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.140525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121628 restraints weight = 3846.229| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.78 r_work: 0.2802 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3534 Z= 0.172 Angle : 0.474 5.760 4804 Z= 0.242 Chirality : 0.044 0.178 536 Planarity : 0.004 0.036 612 Dihedral : 4.916 49.328 617 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.38 % Allowed : 8.26 % 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: -0.15 (0.42), residues: 427 helix: -3.85 (0.61), residues: 33 sheet: 0.32 (0.42), residues: 157 loop : 0.33 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS L 92 PHE 0.006 0.001 PHE H 29 TYR 0.011 0.001 TYR A 369 ARG 0.002 0.000 ARG H 38 *********************** 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 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.396 Fit side-chains REVERT: A 378 LYS cc_start: 0.8807 (mttt) cc_final: 0.8032 (mtmt) REVERT: A 471 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8247 (mt-10) REVERT: H 43 GLN cc_start: 0.8552 (mm110) cc_final: 0.8253 (mp10) REVERT: H 70 MET cc_start: 0.9312 (mtt) cc_final: 0.8699 (mtt) REVERT: L 82 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7921 (pm20) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.1086 time to fit residues: 5.7883 Evaluate side-chains 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3108 r_free = 0.3108 target = 0.110266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.093307 restraints weight = 4127.354| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.57 r_work: 0.2779 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2973 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= 0.342 Angle : 0.544 7.054 4804 Z= 0.275 Chirality : 0.046 0.145 536 Planarity : 0.004 0.040 612 Dihedral : 4.903 39.597 617 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.48 % Allowed : 6.89 % Favored : 90.63 % 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: -0.26 (0.42), residues: 427 helix: -3.81 (0.64), residues: 33 sheet: 0.28 (0.42), residues: 157 loop : 0.21 (0.44), 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 0.009 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 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.406 Fit side-chains REVERT: A 378 LYS cc_start: 0.8820 (mttt) cc_final: 0.8055 (mtmt) REVERT: A 471 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8234 (mt-10) REVERT: H 70 MET cc_start: 0.9331 (mtt) cc_final: 0.8637 (mtt) REVERT: L 82 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7940 (pm20) outliers start: 9 outliers final: 7 residues processed: 33 average time/residue: 0.1051 time to fit residues: 5.0127 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 : 0.393 ------------------------------------------------------------------------------- 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: 0.3980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.0980 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 = 0.3134 r_free = 0.3134 target = 0.112382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.097014 restraints weight = 3986.971| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.42 r_work: 0.2827 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3534 Z= 0.229 Angle : 0.501 8.644 4804 Z= 0.253 Chirality : 0.045 0.217 536 Planarity : 0.004 0.036 612 Dihedral : 4.568 31.929 617 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.93 % Allowed : 7.44 % Favored : 90.63 % 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 (0.43), residues: 427 helix: -3.55 (0.74), residues: 27 sheet: 0.32 (0.42), residues: 157 loop : 0.35 (0.44), residues: 243 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 H 29 TYR 0.011 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 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.369 Fit side-chains REVERT: A 378 LYS cc_start: 0.8803 (mttt) cc_final: 0.8061 (mtmt) REVERT: A 471 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8240 (mt-10) REVERT: H 43 GLN cc_start: 0.8568 (mp10) cc_final: 0.8233 (mp10) REVERT: H 70 MET cc_start: 0.9312 (mtt) cc_final: 0.8682 (mtt) REVERT: L 82 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7916 (pm20) outliers start: 7 outliers final: 5 residues processed: 36 average time/residue: 0.1050 time to fit residues: 5.4196 Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.6980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 13 optimal weight: 0.0770 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.138807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.120000 restraints weight = 3867.235| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.78 r_work: 0.2780 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3534 Z= 0.246 Angle : 0.503 7.110 4804 Z= 0.254 Chirality : 0.045 0.184 536 Planarity : 0.004 0.037 612 Dihedral : 4.658 34.702 617 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.38 % Allowed : 7.99 % Favored : 90.63 % 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 (0.43), residues: 427 helix: -3.53 (0.74), residues: 27 sheet: 0.32 (0.42), residues: 157 loop : 0.34 (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 0.012 0.001 TYR A 495 ARG 0.002 0.000 ARG H 38 ********************** 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 32 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.333 Fit side-chains REVERT: A 378 LYS cc_start: 0.8751 (mttt) cc_final: 0.7975 (mtmt) REVERT: A 471 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8268 (mt-10) REVERT: H 43 GLN cc_start: 0.8532 (mp10) cc_final: 0.8174 (mp10) REVERT: H 70 MET cc_start: 0.9319 (mtt) cc_final: 0.8656 (mtt) outliers start: 5 outliers final: 5 residues processed: 32 average time/residue: 0.1006 time to fit residues: 4.6883 Evaluate side-chains 32 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 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 = 0.3483 r_free = 0.3483 target = 0.137503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.118983 restraints weight = 3917.469| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.77 r_work: 0.2771 rms_B_bonded: 2.18 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: 0.8710 moved from start: 0.3133 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= 0.269 Angle : 0.512 6.858 4804 Z= 0.259 Chirality : 0.045 0.157 536 Planarity : 0.004 0.037 612 Dihedral : 4.767 35.504 617 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.93 % Allowed : 7.44 % Favored : 90.63 % 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: -0.02 (0.43), residues: 427 helix: -3.48 (0.77), residues: 27 sheet: 0.31 (0.42), residues: 157 loop : 0.34 (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 A 429 TYR 0.013 0.001 TYR A 495 ARG 0.002 0.000 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.63 seconds wall clock time: 43 minutes 42.17 seconds (2622.17 seconds total)