Starting phenix.real_space_refine (version: dev) on Sun Dec 11 13:38:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/12_2022/7n5f_24188_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/12_2022/7n5f_24188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/12_2022/7n5f_24188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/12_2022/7n5f_24188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/12_2022/7n5f_24188_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5f_24188/12_2022/7n5f_24188_updated.pdb" } resolution = 2.7 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= 0.001 sd= 0.027 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 Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 3037 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3037 Unusual residues: {'PLM': 1} Classifications: {'peptide': 386, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378, None: 1} Not linked: pdbres="ASN A 751 " pdbres="PLM A 801 " Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Time building chain proxies: 2.32, per 1000 atoms: 0.76 Number of scatterers: 3037 At special positions: 0 Unit cell: (56.65, 90.64, 141.11, 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 12 16.00 O 526 8.00 N 503 7.00 C 1996 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: 1.35 Conformation dependent library (CDL) restraints added in 421.4 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 61.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 223 through 243 removed outlier: 4.233A pdb=" N LEU A 226 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 282 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 332 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 Processing helix chain 'A' and resid 504 through 551 Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 631 through 636 removed outlier: 4.907A pdb=" N THR A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 Processing helix chain 'A' and resid 715 through 736 Processing sheet with id= A, first strand: chain 'A' and resid 639 through 641 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.783A pdb=" N ALA A 703 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL A 691 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 705 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N MET A 689 " --> pdb=" O PHE A 705 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 707 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N HIS A 687 " --> pdb=" O ASN A 707 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 579 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: 0.81 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 566 1.31 - 1.44: 824 1.44 - 1.56: 1667 1.56 - 1.69: 16 1.69 - 1.82: 21 Bond restraints: 3094 Sorted by residual: bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.39e+01 bond pdb=" CB ILE A 285 " pdb=" CG1 ILE A 285 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" NE1 TRP A 273 " pdb=" CE2 TRP A 273 " ideal model delta sigma weight residual 1.370 1.315 0.055 1.10e-02 8.26e+03 2.52e+01 bond pdb=" CB LEU A 258 " pdb=" CG LEU A 258 " ideal model delta sigma weight residual 1.530 1.628 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CB TYR A 629 " pdb=" CG TYR A 629 " ideal model delta sigma weight residual 1.512 1.406 0.106 2.20e-02 2.07e+03 2.34e+01 ... (remaining 3089 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.20: 63 106.20 - 113.17: 1680 113.17 - 120.13: 1293 120.13 - 127.10: 1120 127.10 - 134.07: 34 Bond angle restraints: 4190 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.07 -8.27 1.00e+00 1.00e+00 6.83e+01 angle pdb=" C LEU A 743 " pdb=" N PRO A 744 " pdb=" CA PRO A 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C HIS A 592 " pdb=" N PRO A 593 " pdb=" CA PRO A 593 " ideal model delta sigma weight residual 119.56 125.29 -5.73 1.01e+00 9.80e-01 3.22e+01 angle pdb=" C SER A 645 " pdb=" N PRO A 646 " pdb=" CA PRO A 646 " ideal model delta sigma weight residual 120.98 126.89 -5.91 1.07e+00 8.73e-01 3.05e+01 angle pdb=" C TYR A 629 " pdb=" N PRO A 630 " pdb=" CA PRO A 630 " ideal model delta sigma weight residual 119.76 125.32 -5.56 1.03e+00 9.43e-01 2.91e+01 ... (remaining 4185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 1782 17.70 - 35.40: 36 35.40 - 53.09: 8 53.09 - 70.79: 2 70.79 - 88.49: 3 Dihedral angle restraints: 1831 sinusoidal: 699 harmonic: 1132 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.65 8.15 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.49 88.49 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 1828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 408 0.108 - 0.216: 84 0.216 - 0.323: 12 0.323 - 0.431: 0 0.431 - 0.539: 2 Chirality restraints: 506 Sorted by residual: chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" CA PHE A 335 " pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CB PHE A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 503 not shown) Planarity restraints: 511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 697 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C VAL A 697 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL A 697 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 329 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C SER A 329 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 329 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 330 " -0.017 2.00e-02 2.50e+03 ... (remaining 508 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 1545 2.95 - 3.44: 3145 3.44 - 3.93: 4812 3.93 - 4.41: 5632 4.41 - 4.90: 8454 Nonbonded interactions: 23588 Sorted by model distance: nonbonded pdb=" N ASN A 711 " pdb=" O ASN A 711 " model vdw 2.468 2.496 nonbonded pdb=" NZ LYS A 730 " pdb=" OE2 GLU A 734 " model vdw 2.473 2.520 nonbonded pdb=" N VAL A 697 " pdb=" N ASN A 698 " model vdw 2.491 2.560 nonbonded pdb=" NZ LYS A 579 " pdb=" OE2 GLU A 583 " model vdw 2.506 2.520 nonbonded pdb=" N THR A 295 " pdb=" N ARG A 296 " model vdw 2.536 2.560 ... (remaining 23583 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 12 5.16 5 C 1996 2.51 5 N 503 2.21 5 O 526 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 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: 1.190 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: 4.510 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 13.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 : 0.023 0.124 3094 Z= 1.462 Angle : 1.502 8.265 4190 Z= 1.032 Chirality : 0.097 0.539 506 Planarity : 0.008 0.037 511 Dihedral : 9.991 88.488 1085 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: 1.68 (0.40), residues: 374 helix: 1.43 (0.29), residues: 242 sheet: 0.14 (0.80), residues: 38 loop : 1.02 (0.67), residues: 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.8853 time to fit residues: 138.8688 Evaluate side-chains 133 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3094 Z= 0.208 Angle : 0.551 6.503 4190 Z= 0.309 Chirality : 0.041 0.132 506 Planarity : 0.004 0.024 511 Dihedral : 5.892 48.385 411 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer Outliers : 4.76 % 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: 3.30 (0.45), residues: 374 helix: 2.91 (0.32), residues: 232 sheet: 0.70 (0.76), residues: 44 loop : 1.21 (0.79), residues: 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.379 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 128 average time/residue: 0.8862 time to fit residues: 117.2245 Evaluate side-chains 127 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.4805 time to fit residues: 2.4936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN A 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 3094 Z= 0.187 Angle : 0.466 6.285 4190 Z= 0.264 Chirality : 0.040 0.145 506 Planarity : 0.003 0.022 511 Dihedral : 5.577 47.307 411 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 5.71 % 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: 2.80 (0.44), residues: 374 helix: 2.68 (0.33), residues: 238 sheet: 0.34 (0.73), residues: 42 loop : 0.47 (0.74), residues: 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.383 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 0.8702 time to fit residues: 114.1053 Evaluate side-chains 123 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 6 average time/residue: 0.5123 time to fit residues: 3.7083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS A 648 GLN A 713 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3094 Z= 0.199 Angle : 0.480 6.267 4190 Z= 0.267 Chirality : 0.041 0.152 506 Planarity : 0.003 0.021 511 Dihedral : 5.503 44.403 411 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 5.71 % 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: 2.67 (0.44), residues: 374 helix: 2.61 (0.33), residues: 238 sheet: 0.28 (0.74), residues: 42 loop : 0.32 (0.73), residues: 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.384 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 124 average time/residue: 0.8884 time to fit residues: 113.7057 Evaluate side-chains 121 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 4 average time/residue: 0.0664 time to fit residues: 0.8612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3094 Z= 0.190 Angle : 0.446 3.981 4190 Z= 0.254 Chirality : 0.040 0.157 506 Planarity : 0.003 0.020 511 Dihedral : 5.412 42.161 411 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 4.76 % 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: 2.56 (0.45), residues: 374 helix: 2.58 (0.33), residues: 238 sheet: 0.27 (0.74), residues: 42 loop : 0.09 (0.72), residues: 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 119 average time/residue: 0.9257 time to fit residues: 113.5884 Evaluate side-chains 119 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.7044 time to fit residues: 4.9535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3094 Z= 0.156 Angle : 0.459 7.754 4190 Z= 0.251 Chirality : 0.040 0.181 506 Planarity : 0.002 0.020 511 Dihedral : 5.223 40.805 411 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 4.13 % 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: 2.65 (0.45), residues: 374 helix: 2.66 (0.33), residues: 238 sheet: 0.29 (0.73), residues: 42 loop : 0.08 (0.73), residues: 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.410 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 124 average time/residue: 0.8712 time to fit residues: 111.5458 Evaluate side-chains 122 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0612 time to fit residues: 0.7680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 3094 Z= 0.163 Angle : 0.436 5.282 4190 Z= 0.246 Chirality : 0.040 0.160 506 Planarity : 0.002 0.019 511 Dihedral : 5.112 40.478 411 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 5.71 % 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: 2.63 (0.44), residues: 374 helix: 2.67 (0.32), residues: 236 sheet: 0.41 (0.75), residues: 42 loop : 0.01 (0.72), residues: 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.372 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 6 residues processed: 121 average time/residue: 0.8729 time to fit residues: 108.9989 Evaluate side-chains 122 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 0.8871 time to fit residues: 5.0827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.0010 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 3094 Z= 0.173 Angle : 0.482 8.457 4190 Z= 0.261 Chirality : 0.042 0.240 506 Planarity : 0.003 0.048 511 Dihedral : 5.075 40.671 411 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 3.49 % 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: 2.65 (0.44), residues: 374 helix: 2.65 (0.33), residues: 236 sheet: 0.64 (0.78), residues: 37 loop : 0.03 (0.70), residues: 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 0.392 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 122 average time/residue: 0.8922 time to fit residues: 112.2747 Evaluate side-chains 127 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 7 average time/residue: 0.4510 time to fit residues: 3.8356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3094 Z= 0.141 Angle : 0.443 5.542 4190 Z= 0.249 Chirality : 0.039 0.165 506 Planarity : 0.003 0.030 511 Dihedral : 4.860 38.858 411 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 2.54 % 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: 2.78 (0.45), residues: 374 helix: 2.74 (0.32), residues: 237 sheet: 0.72 (0.80), residues: 37 loop : 0.05 (0.72), residues: 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.387 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 118 average time/residue: 0.9270 time to fit residues: 112.7378 Evaluate side-chains 117 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.359 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3903 time to fit residues: 1.7481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3094 Z= 0.191 Angle : 0.497 8.724 4190 Z= 0.267 Chirality : 0.041 0.173 506 Planarity : 0.003 0.025 511 Dihedral : 4.941 41.454 411 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 1.90 % 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: 2.88 (0.45), residues: 374 helix: 2.85 (0.32), residues: 231 sheet: 0.89 (0.77), residues: 39 loop : 0.12 (0.72), residues: 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 0.400 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 120 average time/residue: 0.9141 time to fit residues: 113.0549 Evaluate side-chains 123 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1039 time to fit residues: 1.0394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.154739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137879 restraints weight = 4505.172| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.01 r_work: 0.3788 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3094 Z= 0.190 Angle : 0.480 5.918 4190 Z= 0.269 Chirality : 0.041 0.168 506 Planarity : 0.003 0.024 511 Dihedral : 4.858 40.319 411 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 0.95 % 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: 2.60 (0.45), residues: 374 helix: 2.65 (0.32), residues: 237 sheet: 0.58 (0.81), residues: 37 loop : -0.10 (0.72), residues: 100 =============================================================================== Job complete usr+sys time: 2170.50 seconds wall clock time: 38 minutes 43.33 seconds (2323.33 seconds total)