Starting phenix.real_space_refine on Fri Aug 2 14:46:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/08_2024/8v4f_42970.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/08_2024/8v4f_42970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/08_2024/8v4f_42970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/08_2024/8v4f_42970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/08_2024/8v4f_42970.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/08_2024/8v4f_42970.cif" } resolution = 2.68 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= -0.000 sd= 0.008 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 14 5.16 5 C 2064 2.51 5 N 548 2.21 5 O 611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3237 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 905 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1530 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain breaks: 1 Time building chain proxies: 2.97, per 1000 atoms: 0.92 Number of scatterers: 3237 At special positions: 0 Unit cell: (72.72, 70.7, 85.85, 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 14 16.00 O 611 8.00 N 548 7.00 C 2064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 576.7 milliseconds 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.1% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.804A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.639A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.751A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.843A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.068A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.668A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.521A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.717A pdb=" N MET B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.931A pdb=" N CYS B 95 " --> pdb=" O TRP B 107 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP B 107 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG B 97 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.846A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.485A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU D 33 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 110 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: 0.85 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1000 1.34 - 1.46: 779 1.46 - 1.58: 1528 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3323 Sorted by residual: bond pdb=" N VAL D 3 " pdb=" CA VAL D 3 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.14e+00 bond pdb=" N PHE A 347 " pdb=" CA PHE A 347 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.22e-02 6.72e+03 6.88e+00 bond pdb=" N ILE D 2 " pdb=" CA ILE D 2 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.68e+00 bond pdb=" N TYR B 106 " pdb=" CA TYR B 106 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.47e+00 bond pdb=" N LEU D 4 " pdb=" CA LEU D 4 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.27e-02 6.20e+03 4.69e+00 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 100.87 - 107.51: 133 107.51 - 114.15: 1680 114.15 - 120.79: 1418 120.79 - 127.42: 1249 127.42 - 134.06: 31 Bond angle restraints: 4511 Sorted by residual: angle pdb=" C GLY D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CG ARG D 61 " pdb=" CD ARG D 61 " pdb=" NE ARG D 61 " ideal model delta sigma weight residual 112.00 120.29 -8.29 2.20e+00 2.07e-01 1.42e+01 angle pdb=" CA TYR D 91 " pdb=" CB TYR D 91 " pdb=" CG TYR D 91 " ideal model delta sigma weight residual 113.90 119.86 -5.96 1.80e+00 3.09e-01 1.10e+01 angle pdb=" C GLU D 17 " pdb=" N ARG D 18 " pdb=" CA ARG D 18 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.75e+00 angle pdb=" C ARG D 18 " pdb=" N ALA D 19 " pdb=" CA ALA D 19 " ideal model delta sigma weight residual 121.87 128.17 -6.30 2.24e+00 1.99e-01 7.91e+00 ... (remaining 4506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 1729 16.86 - 33.72: 175 33.72 - 50.58: 35 50.58 - 67.44: 5 67.44 - 84.30: 3 Dihedral angle restraints: 1947 sinusoidal: 762 harmonic: 1185 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 58.90 34.10 1 1.00e+01 1.00e-02 1.65e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual -73.00 -13.63 -59.37 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 70 " pdb=" CB ASP D 70 " pdb=" CG ASP D 70 " pdb=" OD1 ASP D 70 " ideal model delta sinusoidal sigma weight residual -30.00 -86.57 56.57 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 1944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 283 0.046 - 0.093: 120 0.093 - 0.139: 52 0.139 - 0.185: 13 0.185 - 0.231: 6 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA TYR D 91 " pdb=" N TYR D 91 " pdb=" C TYR D 91 " pdb=" CB TYR D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB THR B 114 " pdb=" CA THR B 114 " pdb=" OG1 THR B 114 " pdb=" CG2 THR B 114 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE B 12 " pdb=" CA ILE B 12 " pdb=" CG1 ILE B 12 " pdb=" CG2 ILE B 12 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 471 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 509 " 0.215 9.50e-02 1.11e+02 9.70e-02 7.24e+00 pdb=" NE ARG A 509 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 509 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 509 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 509 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 79 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO D 80 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 468 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C ILE A 468 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 468 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 469 " -0.012 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1163 2.87 - 3.38: 2685 3.38 - 3.88: 5539 3.88 - 4.39: 6229 4.39 - 4.90: 10738 Nonbonded interactions: 26354 Sorted by model distance: nonbonded pdb=" OG SER B 56 " pdb=" OD2 ASP A 420 " model vdw 2.360 3.040 nonbonded pdb=" OH TYR B 33 " pdb=" O LEU A 455 " model vdw 2.366 3.040 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.368 3.040 nonbonded pdb=" OD1 ASN A 448 " pdb=" ND2 ASN A 450 " model vdw 2.391 3.120 nonbonded pdb=" O TYR B 52 " pdb=" NH2 ARG B 71 " model vdw 2.394 3.120 ... (remaining 26349 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: 2.590 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.260 Find NCS groups from input model: 0.040 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:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3323 Z= 0.333 Angle : 0.991 8.572 4511 Z= 0.539 Chirality : 0.064 0.231 474 Planarity : 0.008 0.097 587 Dihedral : 13.785 84.298 1181 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.42), residues: 404 helix: -1.61 (1.32), residues: 13 sheet: 0.46 (0.44), residues: 135 loop : -0.60 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 36 HIS 0.003 0.001 HIS A 505 PHE 0.024 0.002 PHE A 464 TYR 0.027 0.003 TYR B 52 ARG 0.021 0.002 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.385 Fit side-chains REVERT: B 18 LEU cc_start: 0.8361 (tp) cc_final: 0.8033 (tp) REVERT: B 30 SER cc_start: 0.8532 (p) cc_final: 0.8295 (t) REVERT: B 59 TYR cc_start: 0.8618 (m-80) cc_final: 0.8065 (m-80) REVERT: B 79 TYR cc_start: 0.8477 (m-80) cc_final: 0.8249 (m-10) REVERT: B 109 GLN cc_start: 0.7499 (pm20) cc_final: 0.6914 (pm20) REVERT: B 112 LEU cc_start: 0.8829 (tp) cc_final: 0.8628 (tm) REVERT: A 342 PHE cc_start: 0.8551 (m-80) cc_final: 0.8331 (m-80) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.8761 time to fit residues: 88.1583 Evaluate side-chains 94 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 20 optimal weight: 0.1980 chunk 31 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3323 Z= 0.190 Angle : 0.532 4.814 4511 Z= 0.280 Chirality : 0.044 0.130 474 Planarity : 0.005 0.054 587 Dihedral : 4.450 17.247 462 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.01 % Allowed : 12.07 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.41), residues: 404 helix: -3.20 (1.03), residues: 14 sheet: 0.75 (0.44), residues: 134 loop : -0.62 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 107 HIS 0.002 0.001 HIS A 505 PHE 0.011 0.001 PHE A 464 TYR 0.011 0.001 TYR B 33 ARG 0.012 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.356 Fit side-chains REVERT: B 18 LEU cc_start: 0.8333 (tp) cc_final: 0.8043 (tt) REVERT: B 19 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7803 (ttt-90) REVERT: B 35 SER cc_start: 0.8841 (m) cc_final: 0.8600 (p) REVERT: B 79 TYR cc_start: 0.8510 (m-80) cc_final: 0.8259 (m-80) REVERT: B 109 GLN cc_start: 0.7338 (pm20) cc_final: 0.6856 (pm20) REVERT: D 61 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7697 (ptp90) REVERT: A 408 ARG cc_start: 0.8234 (ptm-80) cc_final: 0.7828 (ptm-80) REVERT: A 498 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7659 (tpp80) outliers start: 7 outliers final: 3 residues processed: 102 average time/residue: 0.8281 time to fit residues: 87.6533 Evaluate side-chains 106 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain A residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 0.0370 chunk 27 optimal weight: 0.3980 chunk 18 optimal weight: 0.0770 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN D 6 GLN A 394 ASN A 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3323 Z= 0.188 Angle : 0.505 4.917 4511 Z= 0.260 Chirality : 0.043 0.125 474 Planarity : 0.004 0.051 587 Dihedral : 4.299 17.782 462 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.16 % Allowed : 14.66 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.42), residues: 404 helix: -2.94 (1.14), residues: 12 sheet: 0.69 (0.45), residues: 135 loop : -0.35 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.012 0.001 PHE A 342 TYR 0.010 0.001 TYR B 33 ARG 0.006 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.349 Fit side-chains REVERT: B 19 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7813 (ttt-90) REVERT: B 35 SER cc_start: 0.8824 (m) cc_final: 0.8575 (p) REVERT: B 109 GLN cc_start: 0.7268 (pm20) cc_final: 0.6816 (pm20) REVERT: D 61 ARG cc_start: 0.8153 (mtm110) cc_final: 0.7834 (ptp90) REVERT: A 377 PHE cc_start: 0.7941 (t80) cc_final: 0.7738 (t80) REVERT: A 409 GLN cc_start: 0.8657 (mt0) cc_final: 0.8366 (mt0) REVERT: A 424 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8115 (tttm) outliers start: 11 outliers final: 4 residues processed: 97 average time/residue: 0.6444 time to fit residues: 65.5847 Evaluate side-chains 99 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain A residue 424 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 0.0980 chunk 0 optimal weight: 0.9980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN D 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3323 Z= 0.256 Angle : 0.536 6.506 4511 Z= 0.273 Chirality : 0.045 0.139 474 Planarity : 0.004 0.053 587 Dihedral : 4.488 18.786 462 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.31 % Allowed : 13.22 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.42), residues: 404 helix: -2.45 (1.28), residues: 12 sheet: 0.57 (0.43), residues: 145 loop : -0.26 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 107 HIS 0.002 0.001 HIS B 3 PHE 0.014 0.001 PHE A 464 TYR 0.011 0.001 TYR A 495 ARG 0.003 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.360 Fit side-chains REVERT: B 19 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7485 (ttt-90) REVERT: B 109 GLN cc_start: 0.7259 (pm20) cc_final: 0.6814 (pm20) REVERT: D 61 ARG cc_start: 0.8120 (mtm110) cc_final: 0.7540 (ptp90) REVERT: D 79 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: A 424 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8175 (ttmm) REVERT: A 425 LEU cc_start: 0.8735 (mt) cc_final: 0.8532 (mt) REVERT: A 438 SER cc_start: 0.8102 (p) cc_final: 0.7884 (p) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.5725 time to fit residues: 61.6004 Evaluate side-chains 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.0050 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3323 Z= 0.383 Angle : 0.594 7.436 4511 Z= 0.304 Chirality : 0.047 0.132 474 Planarity : 0.005 0.057 587 Dihedral : 4.886 21.395 462 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.89 % Allowed : 13.22 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.42), residues: 404 helix: -1.95 (1.48), residues: 12 sheet: 0.50 (0.43), residues: 146 loop : -0.33 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 107 HIS 0.002 0.001 HIS A 505 PHE 0.019 0.002 PHE A 392 TYR 0.013 0.002 TYR A 423 ARG 0.004 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.366 Fit side-chains REVERT: B 19 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7520 (ttt-90) REVERT: B 35 SER cc_start: 0.8814 (m) cc_final: 0.8586 (p) REVERT: B 38 ARG cc_start: 0.8664 (ptt180) cc_final: 0.8147 (ptt180) REVERT: B 109 GLN cc_start: 0.7271 (pm20) cc_final: 0.6815 (pm20) REVERT: D 6 GLN cc_start: 0.8356 (mt0) cc_final: 0.8154 (mt0) REVERT: D 79 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6078 (mp0) REVERT: A 335 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7661 (mt) REVERT: A 357 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8021 (tpt-90) REVERT: A 377 PHE cc_start: 0.7948 (t80) cc_final: 0.7735 (t80) REVERT: A 424 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8219 (tttm) REVERT: A 438 SER cc_start: 0.8078 (p) cc_final: 0.7859 (p) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.6235 time to fit residues: 68.1420 Evaluate side-chains 111 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 22 optimal weight: 0.0980 chunk 28 optimal weight: 0.0980 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN D 37 GLN A 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3323 Z= 0.171 Angle : 0.505 6.424 4511 Z= 0.256 Chirality : 0.043 0.129 474 Planarity : 0.004 0.050 587 Dihedral : 4.429 20.407 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.87 % Allowed : 18.10 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.43), residues: 404 helix: -1.85 (1.53), residues: 12 sheet: 0.47 (0.43), residues: 145 loop : -0.17 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.000 HIS B 3 PHE 0.011 0.001 PHE A 377 TYR 0.011 0.001 TYR B 33 ARG 0.008 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.343 Fit side-chains REVERT: B 19 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7803 (ttt-90) REVERT: B 35 SER cc_start: 0.8764 (m) cc_final: 0.8544 (p) REVERT: B 59 TYR cc_start: 0.8496 (m-80) cc_final: 0.8269 (m-80) REVERT: B 80 LEU cc_start: 0.8824 (tp) cc_final: 0.8491 (tp) REVERT: B 109 GLN cc_start: 0.7302 (pm20) cc_final: 0.6839 (pm20) REVERT: D 61 ARG cc_start: 0.7948 (mtm110) cc_final: 0.7645 (ptp90) REVERT: D 79 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: A 438 SER cc_start: 0.7972 (p) cc_final: 0.7742 (p) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 0.6039 time to fit residues: 62.8911 Evaluate side-chains 108 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 0.0970 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3323 Z= 0.199 Angle : 0.508 6.982 4511 Z= 0.259 Chirality : 0.044 0.128 474 Planarity : 0.004 0.049 587 Dihedral : 4.417 21.574 462 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.74 % Allowed : 16.95 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.42), residues: 404 helix: -1.94 (1.50), residues: 12 sheet: 0.56 (0.45), residues: 135 loop : -0.18 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 107 HIS 0.001 0.000 HIS B 3 PHE 0.017 0.001 PHE A 377 TYR 0.011 0.001 TYR B 33 ARG 0.008 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.379 Fit side-chains REVERT: B 19 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7822 (ttt-90) REVERT: B 35 SER cc_start: 0.8759 (m) cc_final: 0.8532 (p) REVERT: B 80 LEU cc_start: 0.8837 (tp) cc_final: 0.8508 (tp) REVERT: B 109 GLN cc_start: 0.7305 (pm20) cc_final: 0.6841 (pm20) REVERT: D 79 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.5993 (mp0) REVERT: A 409 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8359 (mt0) REVERT: A 438 SER cc_start: 0.7974 (p) cc_final: 0.7718 (p) outliers start: 13 outliers final: 7 residues processed: 100 average time/residue: 0.6347 time to fit residues: 66.6771 Evaluate side-chains 107 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3323 Z= 0.331 Angle : 0.577 7.134 4511 Z= 0.292 Chirality : 0.046 0.129 474 Planarity : 0.005 0.053 587 Dihedral : 4.772 23.624 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.74 % Allowed : 17.24 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.42), residues: 404 helix: -1.73 (1.54), residues: 12 sheet: 0.46 (0.43), residues: 145 loop : -0.24 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.018 0.002 PHE A 392 TYR 0.013 0.002 TYR D 91 ARG 0.014 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.374 Fit side-chains REVERT: B 19 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7480 (ttt-90) REVERT: B 35 SER cc_start: 0.8797 (m) cc_final: 0.8563 (p) REVERT: B 38 ARG cc_start: 0.8670 (ptt180) cc_final: 0.8195 (ptt180) REVERT: B 109 GLN cc_start: 0.7294 (pm20) cc_final: 0.6823 (pm20) REVERT: D 79 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: A 357 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8075 (tpt-90) REVERT: A 438 SER cc_start: 0.8009 (p) cc_final: 0.7754 (p) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.5961 time to fit residues: 59.0970 Evaluate side-chains 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 39 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 19 optimal weight: 0.1980 chunk 25 optimal weight: 0.0980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3323 Z= 0.233 Angle : 0.540 7.129 4511 Z= 0.273 Chirality : 0.044 0.124 474 Planarity : 0.005 0.050 587 Dihedral : 4.615 23.296 462 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.87 % Allowed : 19.54 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.42), residues: 404 helix: -1.76 (1.52), residues: 12 sheet: 0.44 (0.43), residues: 145 loop : -0.22 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 107 HIS 0.001 0.000 HIS B 3 PHE 0.026 0.001 PHE A 377 TYR 0.012 0.001 TYR A 423 ARG 0.015 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.356 Fit side-chains REVERT: B 19 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7825 (ttt-90) REVERT: B 35 SER cc_start: 0.8754 (m) cc_final: 0.8546 (p) REVERT: B 80 LEU cc_start: 0.8850 (tp) cc_final: 0.8503 (tp) REVERT: B 109 GLN cc_start: 0.7308 (pm20) cc_final: 0.6836 (pm20) REVERT: D 61 ARG cc_start: 0.7963 (mtm110) cc_final: 0.7559 (ptp90) REVERT: D 79 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: A 409 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: A 438 SER cc_start: 0.7966 (p) cc_final: 0.7712 (p) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.6299 time to fit residues: 62.8636 Evaluate side-chains 102 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3323 Z= 0.323 Angle : 0.582 7.257 4511 Z= 0.296 Chirality : 0.046 0.124 474 Planarity : 0.005 0.052 587 Dihedral : 4.821 24.750 462 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.45 % Allowed : 19.25 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.42), residues: 404 helix: -1.68 (1.57), residues: 12 sheet: 0.41 (0.43), residues: 145 loop : -0.28 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.017 0.002 PHE A 392 TYR 0.016 0.002 TYR A 423 ARG 0.015 0.001 ARG D 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 808 Ramachandran restraints generated. 404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.384 Fit side-chains REVERT: B 19 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7460 (ttt-90) REVERT: B 35 SER cc_start: 0.8792 (m) cc_final: 0.8574 (p) REVERT: B 66 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8523 (ptm-80) REVERT: B 109 GLN cc_start: 0.7297 (pm20) cc_final: 0.6815 (pm20) REVERT: D 79 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: A 409 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: A 438 SER cc_start: 0.7993 (p) cc_final: 0.7732 (p) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.6704 time to fit residues: 66.8197 Evaluate side-chains 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN A 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126694 restraints weight = 4651.099| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.83 r_work: 0.3611 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3323 Z= 0.354 Angle : 0.597 7.066 4511 Z= 0.302 Chirality : 0.046 0.127 474 Planarity : 0.005 0.053 587 Dihedral : 4.910 25.322 462 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.02 % Allowed : 18.97 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.42), residues: 404 helix: -1.66 (1.58), residues: 12 sheet: 0.42 (0.43), residues: 145 loop : -0.33 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.031 0.002 PHE A 377 TYR 0.015 0.002 TYR A 423 ARG 0.016 0.001 ARG D 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.29 seconds wall clock time: 36 minutes 48.78 seconds (2208.78 seconds total)