Starting phenix.real_space_refine on Thu Jul 18 19:20:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/07_2024/8v4f_42970.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/07_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_42970/07_2024/8v4f_42970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/07_2024/8v4f_42970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/07_2024/8v4f_42970.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4f_42970/07_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-5388/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: 3.09, per 1000 atoms: 0.95 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 566.1 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: 0.47 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: 1.36 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 2.440 nonbonded pdb=" OH TYR B 33 " pdb=" O LEU A 455 " model vdw 2.366 2.440 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.368 2.440 nonbonded pdb=" OD1 ASN A 448 " pdb=" ND2 ASN A 450 " model vdw 2.391 2.520 nonbonded pdb=" O TYR B 52 " pdb=" NH2 ARG B 71 " model vdw 2.394 2.520 ... (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 ========== 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: 2.580 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.140 ------------------------------------------------------------------------------- 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 : 0.318 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: 0.8363 time to fit residues: 84.1729 Evaluate side-chains 94 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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: 0.2980 chunk 30 optimal weight: 0.0060 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 overall best weight: 0.1472 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1526 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= 0.166 Angle : 0.509 4.811 4511 Z= 0.266 Chirality : 0.043 0.131 474 Planarity : 0.005 0.052 587 Dihedral : 4.276 16.893 462 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.87 % Allowed : 10.34 % Favored : 86.78 % 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: -0.36 (0.41), residues: 404 helix: -3.21 (1.02), 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 0.010 0.001 PHE A 464 TYR 0.011 0.001 TYR B 33 ARG 0.011 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 108 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.351 Fit side-chains REVERT: B 18 LEU cc_start: 0.8324 (tp) cc_final: 0.7969 (tt) REVERT: B 19 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7767 (ttt-90) REVERT: B 79 TYR cc_start: 0.8434 (m-80) cc_final: 0.8202 (m-80) REVERT: B 109 GLN cc_start: 0.7247 (pm20) cc_final: 0.6756 (pm20) REVERT: B 112 LEU cc_start: 0.8835 (tp) cc_final: 0.8632 (tm) REVERT: D 61 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7669 (ptp90) REVERT: A 408 ARG cc_start: 0.8262 (ptm-80) cc_final: 0.7871 (ptm-80) REVERT: A 409 GLN cc_start: 0.8528 (mt0) cc_final: 0.8271 (mt0) REVERT: A 424 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8062 (tttm) REVERT: A 438 SER cc_start: 0.8221 (p) cc_final: 0.7975 (p) REVERT: A 498 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7643 (tpp80) outliers start: 10 outliers final: 4 residues processed: 101 average time/residue: 0.7691 time to fit residues: 80.9286 Evaluate side-chains 107 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER 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 Chi-restraints excluded: chain A residue 424 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 6 GLN D 89 GLN A 343 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3323 Z= 0.362 Angle : 0.593 7.061 4511 Z= 0.307 Chirality : 0.046 0.125 474 Planarity : 0.005 0.058 587 Dihedral : 4.788 19.487 462 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.02 % Allowed : 13.79 % 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: -0.38 (0.42), residues: 404 helix: -2.66 (1.18), residues: 12 sheet: 0.53 (0.43), residues: 146 loop : -0.60 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 107 HIS 0.002 0.001 HIS A 505 PHE 0.019 0.002 PHE A 464 TYR 0.016 0.002 TYR A 495 ARG 0.005 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 109 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.320 Fit side-chains REVERT: B 19 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7552 (ttt-90) REVERT: B 109 GLN cc_start: 0.7155 (pm20) cc_final: 0.6710 (pm20) REVERT: B 112 LEU cc_start: 0.8870 (tp) cc_final: 0.8669 (tm) REVERT: D 61 ARG cc_start: 0.8153 (mtm110) cc_final: 0.7813 (ptp90) REVERT: D 79 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: A 377 PHE cc_start: 0.7936 (t80) cc_final: 0.7717 (t80) REVERT: A 438 SER cc_start: 0.8066 (p) cc_final: 0.7817 (p) outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 0.7232 time to fit residues: 76.2560 Evaluate side-chains 104 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 28 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 395 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 6 GLN D 37 GLN A 394 ASN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3323 Z= 0.225 Angle : 0.513 5.090 4511 Z= 0.263 Chirality : 0.043 0.122 474 Planarity : 0.004 0.053 587 Dihedral : 4.448 19.270 462 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.02 % Allowed : 15.52 % Favored : 80.46 % 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: -0.29 (0.42), residues: 404 helix: -1.94 (1.41), residues: 12 sheet: 0.55 (0.43), residues: 144 loop : -0.54 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.001 PHE A 392 TYR 0.012 0.001 TYR B 33 ARG 0.004 0.001 ARG A 357 *********************** 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 103 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7843 (ttt-90) REVERT: B 59 TYR cc_start: 0.8526 (m-80) cc_final: 0.8089 (m-80) REVERT: D 61 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7798 (ptp90) REVERT: A 355 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7808 (tpp-160) REVERT: A 377 PHE cc_start: 0.7909 (t80) cc_final: 0.7691 (t80) REVERT: A 394 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7693 (m-40) REVERT: A 424 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8128 (ttmm) REVERT: A 438 SER cc_start: 0.7974 (p) cc_final: 0.7702 (p) outliers start: 14 outliers final: 5 residues processed: 97 average time/residue: 0.6873 time to fit residues: 69.7990 Evaluate side-chains 98 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 355 ARG Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 22 optimal weight: 0.0870 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 37 GLN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3323 Z= 0.280 Angle : 0.551 6.557 4511 Z= 0.279 Chirality : 0.044 0.138 474 Planarity : 0.004 0.053 587 Dihedral : 4.523 19.592 462 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.60 % Allowed : 16.67 % Favored : 78.74 % 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: -0.33 (0.42), residues: 404 helix: -1.80 (1.47), residues: 12 sheet: 0.44 (0.43), residues: 145 loop : -0.51 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.013 0.001 PHE A 392 TYR 0.013 0.001 TYR B 33 ARG 0.002 0.000 ARG A 498 *********************** 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 104 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7506 (ttt-90) REVERT: B 34 MET cc_start: 0.8591 (mmt) cc_final: 0.8389 (mmt) REVERT: B 59 TYR cc_start: 0.8526 (m-80) cc_final: 0.8215 (m-80) REVERT: D 61 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7801 (ptp90) REVERT: D 79 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: A 377 PHE cc_start: 0.7923 (t80) cc_final: 0.7722 (t80) REVERT: A 424 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8142 (ttmm) REVERT: A 438 SER cc_start: 0.7972 (p) cc_final: 0.7695 (p) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 0.6689 time to fit residues: 65.6455 Evaluate side-chains 97 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 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 67 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 458 LYS 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: 0.0980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 37 GLN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3323 Z= 0.438 Angle : 0.632 8.772 4511 Z= 0.321 Chirality : 0.047 0.138 474 Planarity : 0.005 0.057 587 Dihedral : 5.003 22.965 462 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.60 % Allowed : 17.24 % Favored : 78.16 % 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: -0.47 (0.41), residues: 404 helix: -1.51 (1.58), residues: 12 sheet: 0.36 (0.43), residues: 146 loop : -0.65 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 107 HIS 0.002 0.001 HIS B 3 PHE 0.019 0.002 PHE A 464 TYR 0.017 0.002 TYR D 91 ARG 0.004 0.001 ARG A 457 *********************** 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 116 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7558 (ttt-90) REVERT: D 6 GLN cc_start: 0.8439 (mt0) cc_final: 0.8231 (mt0) REVERT: D 61 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7844 (ptp90) REVERT: D 79 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: A 357 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8067 (tpt-90) REVERT: A 377 PHE cc_start: 0.7963 (t80) cc_final: 0.7756 (t80) REVERT: A 409 GLN cc_start: 0.8656 (mt0) cc_final: 0.8372 (mt0) REVERT: A 438 SER cc_start: 0.7977 (p) cc_final: 0.7721 (p) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.6871 time to fit residues: 74.7907 Evaluate side-chains 110 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 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 67 SER Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 97 THR 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 458 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 37 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2698 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= 0.255 Angle : 0.550 7.229 4511 Z= 0.276 Chirality : 0.044 0.125 474 Planarity : 0.004 0.054 587 Dihedral : 4.672 22.685 462 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.31 % Allowed : 18.97 % Favored : 76.72 % 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: -0.34 (0.42), residues: 404 helix: -1.38 (1.57), residues: 12 sheet: 0.33 (0.43), residues: 145 loop : -0.48 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 107 HIS 0.001 0.001 HIS B 3 PHE 0.013 0.001 PHE A 392 TYR 0.012 0.001 TYR B 33 ARG 0.004 0.000 ARG A 357 *********************** 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 107 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.5618 (tp40) cc_final: 0.5109 (tp40) REVERT: B 19 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7472 (ttt-90) REVERT: D 79 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: A 377 PHE cc_start: 0.7945 (t80) cc_final: 0.7744 (t80) REVERT: A 424 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8150 (ttmm) REVERT: A 438 SER cc_start: 0.7922 (p) cc_final: 0.7641 (p) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 0.6510 time to fit residues: 66.9616 Evaluate side-chains 101 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 67 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 424 LYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 35 optimal weight: 0.0970 chunk 36 optimal weight: 0.0170 chunk 33 optimal weight: 0.1980 chunk 21 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 overall best weight: 0.1154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 37 GLN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3323 Z= 0.141 Angle : 0.489 6.776 4511 Z= 0.247 Chirality : 0.043 0.126 474 Planarity : 0.004 0.051 587 Dihedral : 4.212 20.633 462 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.30 % Allowed : 20.69 % 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: -0.16 (0.42), residues: 404 helix: -1.48 (1.54), residues: 12 sheet: 0.61 (0.44), residues: 131 loop : -0.40 (0.39), residues: 261 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 0.007 0.001 PHE A 377 TYR 0.010 0.001 TYR B 33 ARG 0.003 0.000 ARG A 357 *********************** 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 97 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.333 Fit side-chains REVERT: B 80 LEU cc_start: 0.8821 (tp) cc_final: 0.8489 (tp) REVERT: D 79 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6060 (mp0) REVERT: A 399 SER cc_start: 0.8765 (m) cc_final: 0.8508 (p) REVERT: A 438 SER cc_start: 0.7852 (p) cc_final: 0.7549 (p) REVERT: A 501 TYR cc_start: 0.8313 (m-10) cc_final: 0.8077 (m-10) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.6420 time to fit residues: 62.0144 Evaluate side-chains 94 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 37 GLN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 0.040 3323 Z= 0.300 Angle : 0.572 7.793 4511 Z= 0.286 Chirality : 0.045 0.126 474 Planarity : 0.004 0.054 587 Dihedral : 4.661 23.484 462 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.30 % Allowed : 22.13 % Favored : 75.57 % 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: -0.29 (0.41), residues: 404 helix: -1.53 (1.52), residues: 12 sheet: 0.44 (0.43), residues: 142 loop : -0.47 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 107 HIS 0.001 0.001 HIS A 505 PHE 0.015 0.002 PHE A 392 TYR 0.018 0.002 TYR D 87 ARG 0.004 0.000 ARG A 357 *********************** 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 95 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.346 Fit side-chains REVERT: B 75 ARG cc_start: 0.6127 (mpp80) cc_final: 0.5902 (mpp80) REVERT: D 79 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: A 377 PHE cc_start: 0.7982 (t80) cc_final: 0.7771 (t80) REVERT: A 409 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: A 438 SER cc_start: 0.7875 (p) cc_final: 0.7581 (p) outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.7258 time to fit residues: 68.2377 Evaluate side-chains 92 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 PHE Chi-restraints excluded: chain A residue 409 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.0270 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 37 GLN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2864 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= 0.244 Angle : 0.550 7.623 4511 Z= 0.275 Chirality : 0.044 0.124 474 Planarity : 0.004 0.053 587 Dihedral : 4.612 23.850 462 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.30 % Allowed : 21.84 % Favored : 75.86 % 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: -0.26 (0.41), residues: 404 helix: -1.52 (1.52), residues: 12 sheet: 0.42 (0.42), residues: 142 loop : -0.42 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.012 0.001 PHE A 377 TYR 0.016 0.001 TYR D 87 ARG 0.004 0.000 ARG A 357 ********************** 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 96 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.357 Fit side-chains REVERT: B 80 LEU cc_start: 0.8880 (tp) cc_final: 0.8543 (tp) REVERT: D 79 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6146 (mp0) REVERT: A 377 PHE cc_start: 0.7987 (t80) cc_final: 0.7756 (t80) REVERT: A 438 SER cc_start: 0.7866 (p) cc_final: 0.7567 (p) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.6648 time to fit residues: 62.8464 Evaluate side-chains 95 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 39 optimal weight: 0.3980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 83 ASN D 37 GLN A 409 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.137210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127862 restraints weight = 4625.685| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.83 r_work: 0.3629 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2840 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= 0.256 Angle : 0.552 7.650 4511 Z= 0.277 Chirality : 0.044 0.124 474 Planarity : 0.004 0.053 587 Dihedral : 4.612 23.721 462 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.16 % Allowed : 20.98 % Favored : 75.86 % 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: -0.28 (0.41), residues: 404 helix: -1.51 (1.52), residues: 12 sheet: 0.38 (0.42), residues: 142 loop : -0.43 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 107 HIS 0.001 0.000 HIS A 505 PHE 0.013 0.001 PHE A 392 TYR 0.017 0.001 TYR D 87 ARG 0.004 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2078.19 seconds wall clock time: 37 minutes 5.24 seconds (2225.24 seconds total)