Starting phenix.real_space_refine on Mon Nov 13 17:01:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/11_2023/7zh3_14720.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/11_2023/7zh3_14720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/11_2023/7zh3_14720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/11_2023/7zh3_14720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/11_2023/7zh3_14720.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/11_2023/7zh3_14720.pdb" } resolution = 2.5 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= 0.186 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 14 5.16 5 C 2082 2.51 5 N 538 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 452": "OD1" <-> "OD2" Residue "D PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 574": "OD1" <-> "OD2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 759": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3301 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2656 Unusual residues: {' ZN': 1} Inner-chain residues flagged as termini: ['pdbres="LEU D 785 "'] Classifications: {'peptide': 330, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 316, None: 1} Not linked: pdbres="LEU D 785 " pdbres=" ZN D1000 " Chain breaks: 5 Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1793 SG CYS D 440 37.260 78.151 22.375 1.00 6.35 S ATOM 1816 SG CYS D 443 38.958 78.902 19.208 1.00 6.36 S ATOM 2191 SG CYS D 506 40.949 77.487 22.051 1.00 6.09 S ATOM 2214 SG CYS D 509 39.607 81.273 22.115 1.00 6.77 S Time building chain proxies: 2.15, per 1000 atoms: 0.65 Number of scatterers: 3301 At special positions: 0 Unit cell: (69.96, 92.22, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 14 16.00 O 666 8.00 N 538 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.20 Conformation dependent library (CDL) restraints added in 560.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " Number of angles added : 6 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 8 sheets defined 39.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.717A pdb=" N ILE D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 Processing helix chain 'D' and resid 143 through 166 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 200 through 222 Processing helix chain 'D' and resid 424 through 431 removed outlier: 3.542A pdb=" N GLN D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.763A pdb=" N LYS D 503 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 737 through 742 removed outlier: 3.867A pdb=" N GLU D 742 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 768 removed outlier: 3.649A pdb=" N SER D 768 " --> pdb=" O LEU D 764 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'D' and resid 82 through 83 removed outlier: 6.505A pdb=" N GLY D 82 " --> pdb=" O THR D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 446 through 453 Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 459 removed outlier: 5.876A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 456 through 459 removed outlier: 5.876A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE D 579 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 504 through 506 Processing sheet with id=AA8, first strand: chain 'D' and resid 535 through 536 187 hydrogen bonds defined for protein. 489 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: 1.09 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 803 1.33 - 1.45: 598 1.45 - 1.57: 1897 1.57 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 3317 Sorted by residual: bond pdb=" C SER D 775 " pdb=" N THR D 776 " ideal model delta sigma weight residual 1.331 1.286 0.045 1.63e-02 3.76e+03 7.78e+00 bond pdb=" CB ARG D 186 " pdb=" CG ARG D 186 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.14e+00 bond pdb=" CB LEU D 159 " pdb=" CG LEU D 159 " ideal model delta sigma weight residual 1.530 1.495 0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" CG LYS D 551 " pdb=" CD LYS D 551 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 bond pdb=" CA ASP D 751 " pdb=" CB ASP D 751 " ideal model delta sigma weight residual 1.536 1.474 0.062 4.10e-02 5.95e+02 2.31e+00 ... (remaining 3312 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.10: 51 105.10 - 112.35: 1709 112.35 - 119.60: 1127 119.60 - 126.85: 1560 126.85 - 134.10: 30 Bond angle restraints: 4477 Sorted by residual: angle pdb=" CA LEU C 15 " pdb=" CB LEU C 15 " pdb=" CG LEU C 15 " ideal model delta sigma weight residual 116.30 124.57 -8.27 3.50e+00 8.16e-02 5.59e+00 angle pdb=" C PHE D 535 " pdb=" CA PHE D 535 " pdb=" CB PHE D 535 " ideal model delta sigma weight residual 110.16 114.38 -4.22 1.83e+00 2.99e-01 5.32e+00 angle pdb=" CA GLN D 433 " pdb=" CB GLN D 433 " pdb=" CG GLN D 433 " ideal model delta sigma weight residual 114.10 118.69 -4.59 2.00e+00 2.50e-01 5.28e+00 angle pdb=" C GLU D 424 " pdb=" CA GLU D 424 " pdb=" CB GLU D 424 " ideal model delta sigma weight residual 110.42 114.98 -4.56 1.99e+00 2.53e-01 5.26e+00 angle pdb=" N ASP D 172 " pdb=" CA ASP D 172 " pdb=" C ASP D 172 " ideal model delta sigma weight residual 111.24 114.11 -2.87 1.29e+00 6.01e-01 4.94e+00 ... (remaining 4472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 1819 15.58 - 31.16: 158 31.16 - 46.74: 34 46.74 - 62.32: 11 62.32 - 77.89: 4 Dihedral angle restraints: 2026 sinusoidal: 838 harmonic: 1188 Sorted by residual: dihedral pdb=" CA PRO D 555 " pdb=" C PRO D 555 " pdb=" N LEU D 556 " pdb=" CA LEU D 556 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG D 486 " pdb=" CD ARG D 486 " pdb=" NE ARG D 486 " pdb=" CZ ARG D 486 " ideal model delta sinusoidal sigma weight residual -90.00 -46.72 -43.28 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CB LYS D 428 " pdb=" CG LYS D 428 " pdb=" CD LYS D 428 " pdb=" CE LYS D 428 " ideal model delta sinusoidal sigma weight residual 60.00 118.40 -58.40 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 434 0.074 - 0.149: 83 0.149 - 0.223: 1 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 519 Sorted by residual: chirality pdb=" CG LEU D 519 " pdb=" CB LEU D 519 " pdb=" CD1 LEU D 519 " pdb=" CD2 LEU D 519 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB VAL D 755 " pdb=" CA VAL D 755 " pdb=" CG1 VAL D 755 " pdb=" CG2 VAL D 755 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA PHE D 535 " pdb=" N PHE D 535 " pdb=" C PHE D 535 " pdb=" CB PHE D 535 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 516 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 189 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO D 190 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 190 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 190 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 177 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO D 178 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 178 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 178 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 505 " -0.020 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE D 505 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE D 505 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 505 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 505 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 505 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 505 " -0.005 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 451 2.75 - 3.29: 2912 3.29 - 3.82: 5767 3.82 - 4.36: 7330 4.36 - 4.90: 11851 Nonbonded interactions: 28311 Sorted by model distance: nonbonded pdb=" OE1 GLN D 454 " pdb=" O HOH D1101 " model vdw 2.209 2.440 nonbonded pdb=" O ALA C 46 " pdb=" O HOH C 101 " model vdw 2.270 2.440 nonbonded pdb=" NZ LYS C 33 " pdb=" OD1 ASP D 502 " model vdw 2.298 2.520 nonbonded pdb=" O LEU C 73 " pdb=" OH TYR D 594 " model vdw 2.306 2.440 nonbonded pdb=" O HOH D1131 " pdb=" O HOH D1132 " model vdw 2.329 2.440 ... (remaining 28306 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: 1.370 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: 7.110 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.670 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.010 0.062 3317 Z= 0.655 Angle : 0.842 8.273 4477 Z= 0.451 Chirality : 0.055 0.371 519 Planarity : 0.007 0.060 566 Dihedral : 13.327 77.893 1252 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -1.40 (0.37), residues: 393 helix: -0.49 (0.40), residues: 130 sheet: -0.68 (0.44), residues: 100 loop : -1.31 (0.44), residues: 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.419 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 68 average time/residue: 1.6199 time to fit residues: 112.6741 Evaluate side-chains 62 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0909 time to fit residues: 0.7203 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3317 Z= 0.141 Angle : 0.468 4.995 4477 Z= 0.253 Chirality : 0.037 0.131 519 Planarity : 0.004 0.034 566 Dihedral : 4.841 33.053 430 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.60 % Allowed : 7.22 % Favored : 91.18 % 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: 0.30 (0.41), residues: 393 helix: 1.55 (0.45), residues: 130 sheet: -0.36 (0.44), residues: 104 loop : -0.44 (0.50), residues: 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.432 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 68 average time/residue: 1.6420 time to fit residues: 114.1872 Evaluate side-chains 62 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0534 time to fit residues: 0.6722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0060 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 210 ASN D 216 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3317 Z= 0.194 Angle : 0.488 4.812 4477 Z= 0.259 Chirality : 0.038 0.125 519 Planarity : 0.004 0.034 566 Dihedral : 4.710 28.559 430 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.60 % Allowed : 9.63 % Favored : 88.77 % 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: 0.79 (0.42), residues: 393 helix: 2.15 (0.45), residues: 130 sheet: -0.18 (0.44), residues: 104 loop : -0.28 (0.50), residues: 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.410 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 1.3871 time to fit residues: 91.1267 Evaluate side-chains 65 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 2 average time/residue: 0.0541 time to fit residues: 0.7033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.0030 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.0370 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3317 Z= 0.257 Angle : 0.529 5.477 4477 Z= 0.276 Chirality : 0.039 0.126 519 Planarity : 0.004 0.034 566 Dihedral : 4.811 27.434 430 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.67 % Allowed : 10.43 % Favored : 86.90 % 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: 0.92 (0.42), residues: 393 helix: 2.26 (0.45), residues: 130 sheet: -0.09 (0.44), residues: 102 loop : -0.22 (0.50), residues: 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.402 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 1.3991 time to fit residues: 94.7405 Evaluate side-chains 72 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 6 average time/residue: 0.2878 time to fit residues: 2.4047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3317 Z= 0.250 Angle : 0.518 5.317 4477 Z= 0.271 Chirality : 0.039 0.127 519 Planarity : 0.004 0.033 566 Dihedral : 4.767 26.665 430 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 10.70 % Favored : 86.90 % 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: 1.00 (0.42), residues: 393 helix: 2.32 (0.45), residues: 130 sheet: -0.04 (0.45), residues: 102 loop : -0.15 (0.51), residues: 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.353 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 1.4160 time to fit residues: 97.2917 Evaluate side-chains 71 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.0477 time to fit residues: 0.7730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3317 Z= 0.394 Angle : 0.613 7.703 4477 Z= 0.315 Chirality : 0.043 0.129 519 Planarity : 0.004 0.036 566 Dihedral : 5.109 28.210 430 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.21 % Allowed : 9.89 % Favored : 86.90 % 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: 0.83 (0.42), residues: 393 helix: 2.06 (0.45), residues: 130 sheet: -0.12 (0.44), residues: 102 loop : -0.17 (0.51), residues: 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.407 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 1.5116 time to fit residues: 105.2519 Evaluate side-chains 71 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 5 average time/residue: 0.6876 time to fit residues: 4.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3317 Z= 0.197 Angle : 0.484 4.898 4477 Z= 0.256 Chirality : 0.037 0.125 519 Planarity : 0.004 0.032 566 Dihedral : 4.640 25.421 430 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.34 % Allowed : 12.03 % Favored : 86.63 % 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: 1.08 (0.42), residues: 393 helix: 2.43 (0.45), residues: 130 sheet: -0.07 (0.44), residues: 102 loop : -0.10 (0.51), residues: 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.389 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 67 average time/residue: 1.4258 time to fit residues: 97.8984 Evaluate side-chains 69 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0541 time to fit residues: 0.6555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3317 Z= 0.197 Angle : 0.493 6.165 4477 Z= 0.259 Chirality : 0.037 0.123 519 Planarity : 0.004 0.032 566 Dihedral : 4.551 23.258 430 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.60 % Allowed : 11.76 % Favored : 86.63 % 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: 1.18 (0.42), residues: 393 helix: 2.59 (0.45), residues: 130 sheet: -0.12 (0.44), residues: 104 loop : -0.03 (0.52), residues: 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.367 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 1.4230 time to fit residues: 96.2500 Evaluate side-chains 67 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0817 time to fit residues: 0.6610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3317 Z= 0.168 Angle : 0.468 6.011 4477 Z= 0.247 Chirality : 0.036 0.124 519 Planarity : 0.003 0.030 566 Dihedral : 4.359 20.222 430 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.87 % Allowed : 11.50 % Favored : 86.63 % 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: 1.32 (0.42), residues: 393 helix: 2.77 (0.45), residues: 130 sheet: -0.02 (0.44), residues: 102 loop : -0.04 (0.51), residues: 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.423 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 1.5053 time to fit residues: 100.2512 Evaluate side-chains 62 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.426 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3317 Z= 0.362 Angle : 0.600 7.194 4477 Z= 0.309 Chirality : 0.041 0.123 519 Planarity : 0.004 0.034 566 Dihedral : 4.898 23.998 430 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.87 % Allowed : 12.03 % Favored : 86.10 % 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: 1.02 (0.42), residues: 393 helix: 2.28 (0.44), residues: 130 sheet: -0.11 (0.44), residues: 102 loop : -0.02 (0.51), residues: 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.358 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 1.4823 time to fit residues: 101.7254 Evaluate side-chains 68 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0609 time to fit residues: 0.7202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.100685 restraints weight = 3063.640| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.32 r_work: 0.2909 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3317 Z= 0.234 Angle : 0.519 6.550 4477 Z= 0.271 Chirality : 0.038 0.122 519 Planarity : 0.004 0.035 566 Dihedral : 4.666 23.630 430 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.07 % Allowed : 12.83 % Favored : 86.10 % 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: 1.16 (0.42), residues: 393 helix: 2.47 (0.45), residues: 130 sheet: -0.08 (0.44), residues: 102 loop : 0.01 (0.50), residues: 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.10 seconds wall clock time: 37 minutes 58.72 seconds (2278.72 seconds total)