Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:22:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/11_2022/7jva_22497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/11_2022/7jva_22497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/11_2022/7jva_22497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/11_2022/7jva_22497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/11_2022/7jva_22497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jva_22497/11_2022/7jva_22497.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.021 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3248 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1495 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.48, per 1000 atoms: 0.76 Number of scatterers: 3248 At special positions: 0 Unit cell: (89.25, 75.6, 70.35, 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 15 16.00 O 617 8.00 N 548 7.00 C 2068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.09 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " 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=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 13.3% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 28 through 32 removed outlier: 4.028A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.358A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.815A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.922A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 5.951A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.530A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 129 hydrogen bonds defined for protein. 285 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: 0.89 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 586 1.31 - 1.45: 1042 1.45 - 1.58: 1682 1.58 - 1.71: 4 1.71 - 1.84: 18 Bond restraints: 3332 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.435 1.476 -0.041 1.10e-02 8.26e+03 1.37e+01 bond pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" C3 NAG B 1 " pdb=" C4 NAG B 1 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" CD GLU H 6 " pdb=" OE2 GLU H 6 " ideal model delta sigma weight residual 1.249 1.182 0.067 1.90e-02 2.77e+03 1.23e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 9.92e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.77: 111 106.77 - 113.54: 1671 113.54 - 120.32: 1366 120.32 - 127.10: 1358 127.10 - 133.88: 33 Bond angle restraints: 4539 Sorted by residual: angle pdb=" CD1 LEU H 86 " pdb=" CG LEU H 86 " pdb=" CD2 LEU H 86 " ideal model delta sigma weight residual 110.80 131.55 -20.75 2.20e+00 2.07e-01 8.89e+01 angle pdb=" CG1 VAL H 2 " pdb=" CB VAL H 2 " pdb=" CG2 VAL H 2 " ideal model delta sigma weight residual 110.80 131.11 -20.31 2.20e+00 2.07e-01 8.52e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.02e+00 9.61e-01 5.60e+01 angle pdb=" C LEU A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.85 126.34 -6.49 1.01e+00 9.80e-01 4.12e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.05 -6.49 1.02e+00 9.61e-01 4.04e+01 ... (remaining 4534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 1845 16.77 - 33.53: 74 33.53 - 50.30: 11 50.30 - 67.06: 6 67.06 - 83.83: 1 Dihedral angle restraints: 1937 sinusoidal: 728 harmonic: 1209 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -36.13 -49.87 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 67.40 25.60 1 1.00e+01 1.00e-02 9.42e+00 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 118.10 -25.10 1 1.00e+01 1.00e-02 9.07e+00 ... (remaining 1934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 423 0.112 - 0.224: 61 0.224 - 0.336: 7 0.336 - 0.448: 3 0.448 - 0.560: 2 Chirality restraints: 496 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.25e+02 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.68e+01 chirality pdb=" CG LEU H 86 " pdb=" CB LEU H 86 " pdb=" CD1 LEU H 86 " pdb=" CD2 LEU H 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.83e+00 ... (remaining 493 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 108 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR H 108 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR H 108 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR H 108 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 108 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 108 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 108 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 108 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.035 2.00e-02 2.50e+03 1.83e-02 6.70e+00 pdb=" CG TYR A 495 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 37 " 0.027 2.00e-02 2.50e+03 1.51e-02 4.59e+00 pdb=" CG TYR L 37 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR L 37 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR L 37 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR L 37 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 37 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR L 37 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 37 " 0.024 2.00e-02 2.50e+03 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1320 2.90 - 3.40: 2801 3.40 - 3.90: 5451 3.90 - 4.40: 6366 4.40 - 4.90: 10508 Nonbonded interactions: 26446 Sorted by model distance: nonbonded pdb=" OD2 ASP L 52 " pdb=" NZ LYS A 378 " model vdw 2.398 2.520 nonbonded pdb=" OE2 GLU H 6 " pdb=" N GLN H 111 " model vdw 2.536 2.520 nonbonded pdb=" N ASN A 440 " pdb=" OD1 ASN A 440 " model vdw 2.551 2.520 nonbonded pdb=" N ASP A 428 " pdb=" OD1 ASP A 428 " model vdw 2.552 2.520 nonbonded pdb=" N CYS H 96 " pdb=" O CYS H 96 " model vdw 2.557 2.496 ... (remaining 26441 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2068 2.51 5 N 548 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.570 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 15.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.016 0.079 3332 Z= 1.008 Angle : 1.502 20.747 4539 Z= 0.991 Chirality : 0.090 0.560 496 Planarity : 0.006 0.034 585 Dihedral : 10.049 83.827 1153 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 0.97 % Favored : 98.79 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.87 (0.43), residues: 412 helix: -4.22 (0.39), residues: 28 sheet: 0.47 (0.42), residues: 154 loop : 1.57 (0.44), residues: 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1891 time to fit residues: 22.0726 Evaluate side-chains 62 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0358 time to fit residues: 0.5615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN A 394 ASN A 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 3332 Z= 0.331 Angle : 0.685 9.084 4539 Z= 0.370 Chirality : 0.048 0.143 496 Planarity : 0.005 0.033 585 Dihedral : 5.181 25.476 484 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 0.97 % Favored : 98.79 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.41), residues: 412 helix: -3.58 (0.63), residues: 28 sheet: 0.30 (0.41), residues: 151 loop : 1.08 (0.42), residues: 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.1481 time to fit residues: 14.5639 Evaluate side-chains 70 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0861 time to fit residues: 1.5310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.0170 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 36 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 HIS A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 3332 Z= 0.177 Angle : 0.617 11.024 4539 Z= 0.317 Chirality : 0.044 0.189 496 Planarity : 0.004 0.037 585 Dihedral : 4.941 23.931 484 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.41), residues: 412 helix: -3.31 (0.72), residues: 28 sheet: 0.24 (0.42), residues: 151 loop : 0.97 (0.41), residues: 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 79 average time/residue: 0.1330 time to fit residues: 13.0123 Evaluate side-chains 60 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1871 time to fit residues: 1.1150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0470 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 0.0030 chunk 35 optimal weight: 0.0000 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.2692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 3332 Z= 0.215 Angle : 0.635 15.780 4539 Z= 0.316 Chirality : 0.045 0.190 496 Planarity : 0.004 0.037 585 Dihedral : 4.780 23.285 484 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.42), residues: 412 helix: -2.82 (0.96), residues: 21 sheet: 0.15 (0.42), residues: 150 loop : 0.74 (0.41), residues: 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.358 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1233 time to fit residues: 11.0415 Evaluate side-chains 64 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0339 time to fit residues: 0.7428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN A 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 3332 Z= 0.240 Angle : 0.636 15.133 4539 Z= 0.315 Chirality : 0.044 0.195 496 Planarity : 0.004 0.038 585 Dihedral : 4.773 24.438 484 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.41), residues: 412 helix: -2.75 (0.98), residues: 21 sheet: -0.00 (0.42), residues: 147 loop : 0.72 (0.40), residues: 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.1331 time to fit residues: 11.7309 Evaluate side-chains 64 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0352 time to fit residues: 0.6778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 3332 Z= 0.315 Angle : 0.657 14.378 4539 Z= 0.333 Chirality : 0.046 0.198 496 Planarity : 0.004 0.054 585 Dihedral : 4.891 25.199 484 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.00 (0.42), residues: 412 helix: -2.72 (0.99), residues: 21 sheet: -0.23 (0.43), residues: 147 loop : 0.59 (0.40), residues: 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.1014 time to fit residues: 9.3031 Evaluate side-chains 67 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0289 time to fit residues: 0.7258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 3332 Z= 0.292 Angle : 0.681 15.722 4539 Z= 0.341 Chirality : 0.045 0.196 496 Planarity : 0.004 0.039 585 Dihedral : 4.838 25.208 484 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.42), residues: 412 helix: -2.37 (1.20), residues: 21 sheet: -0.43 (0.45), residues: 140 loop : 0.45 (0.39), residues: 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.386 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.1091 time to fit residues: 9.1376 Evaluate side-chains 61 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0000 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 28 optimal weight: 0.5980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 3332 Z= 0.192 Angle : 0.640 14.472 4539 Z= 0.318 Chirality : 0.043 0.183 496 Planarity : 0.003 0.039 585 Dihedral : 4.625 26.844 484 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.42), residues: 412 helix: -2.66 (1.04), residues: 21 sheet: -0.19 (0.46), residues: 138 loop : 0.48 (0.40), residues: 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.405 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 66 average time/residue: 0.1130 time to fit residues: 9.9195 Evaluate side-chains 61 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0352 time to fit residues: 0.6302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 0.2980 chunk 23 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 3332 Z= 0.233 Angle : 0.658 14.233 4539 Z= 0.325 Chirality : 0.044 0.192 496 Planarity : 0.004 0.038 585 Dihedral : 4.586 26.668 484 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.42), residues: 412 helix: -2.75 (1.03), residues: 21 sheet: -0.10 (0.45), residues: 146 loop : 0.51 (0.41), residues: 245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.293 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1099 time to fit residues: 8.9741 Evaluate side-chains 58 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.446 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.0060 chunk 33 optimal weight: 0.0980 chunk 6 optimal weight: 0.0370 overall best weight: 0.1474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 3332 Z= 0.181 Angle : 0.643 13.981 4539 Z= 0.316 Chirality : 0.043 0.179 496 Planarity : 0.003 0.038 585 Dihedral : 4.464 25.822 484 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.42), residues: 412 helix: -2.79 (1.03), residues: 21 sheet: -0.05 (0.47), residues: 133 loop : 0.46 (0.39), residues: 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.374 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1106 time to fit residues: 9.0182 Evaluate side-chains 57 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.0030 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.0570 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 0.1906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.113809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104656 restraints weight = 5873.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107007 restraints weight = 3256.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108607 restraints weight = 2074.178| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 3332 Z= 0.192 Angle : 0.649 13.605 4539 Z= 0.316 Chirality : 0.044 0.183 496 Planarity : 0.003 0.038 585 Dihedral : 4.465 25.740 484 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.01 (0.42), residues: 412 helix: -3.35 (0.81), residues: 27 sheet: -0.05 (0.46), residues: 139 loop : 0.60 (0.41), residues: 246 =============================================================================== Job complete usr+sys time: 1322.67 seconds wall clock time: 24 minutes 43.51 seconds (1483.51 seconds total)