Starting phenix.real_space_refine (version: dev) on Sun Dec 11 14:52:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/12_2022/7mkm_23899.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/12_2022/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/12_2022/7mkm_23899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/12_2022/7mkm_23899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/12_2022/7mkm_23899.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/12_2022/7mkm_23899.pdb" } resolution = 3.16 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 85": "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: 3192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.37, per 1000 atoms: 0.74 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 67.28, 98.6, 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 17 16.00 O 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 490.2 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 11.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.810A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.100A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.734A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.607A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.771A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.688A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 198 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: 0.75 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1009 1.34 - 1.46: 881 1.46 - 1.58: 1364 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" CA MET L 77 " pdb=" CB MET L 77 " ideal model delta sigma weight residual 1.513 1.536 -0.023 2.59e-02 1.49e+03 7.75e-01 bond pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 1.471 1.484 -0.013 1.74e-02 3.30e+03 5.56e-01 bond pdb=" CB PRO L 94 " pdb=" CG PRO L 94 " ideal model delta sigma weight residual 1.506 1.478 0.028 3.90e-02 6.57e+02 5.29e-01 bond pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.37e-02 5.33e+03 5.16e-01 bond pdb=" CA THR L 68 " pdb=" C THR L 68 " ideal model delta sigma weight residual 1.525 1.536 -0.011 1.63e-02 3.76e+03 4.59e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.89: 103 106.89 - 113.66: 1679 113.66 - 120.44: 1220 120.44 - 127.22: 1417 127.22 - 134.00: 38 Bond angle restraints: 4457 Sorted by residual: angle pdb=" C ARG L 76 " pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 122.04 130.76 -8.72 2.11e+00 2.25e-01 1.71e+01 angle pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " pdb=" CG ARG L 60 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" C LEU H 67 " pdb=" N SER H 68 " pdb=" CA SER H 68 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.83e+00 2.99e-01 6.87e+00 angle pdb=" C GLY L 65 " pdb=" N CYS L 66 " pdb=" CA CYS L 66 " ideal model delta sigma weight residual 122.59 126.34 -3.75 1.57e+00 4.06e-01 5.70e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1738 17.71 - 35.41: 159 35.41 - 53.12: 21 53.12 - 70.82: 0 70.82 - 88.53: 2 Dihedral angle restraints: 1920 sinusoidal: 743 harmonic: 1177 Sorted by residual: dihedral pdb=" CA MET L 77 " pdb=" C MET L 77 " pdb=" N GLU L 78 " pdb=" CA GLU L 78 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR H 59 " pdb=" C TYR H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP L 81 " pdb=" C ASP L 81 " pdb=" N ALA L 82 " pdb=" CA ALA L 82 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 1917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 314 0.037 - 0.074: 111 0.074 - 0.111: 37 0.111 - 0.147: 16 0.147 - 0.184: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 491 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.018 2.00e-02 2.50e+03 1.74e-02 3.80e+00 pdb=" CG ASN A 343 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.96e+00 pdb=" NE ARG A 466 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.000 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 130 2.72 - 3.27: 3159 3.27 - 3.81: 4603 3.81 - 4.36: 5272 4.36 - 4.90: 9289 Nonbonded interactions: 22453 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.177 2.440 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.274 2.440 nonbonded pdb=" O ASN A 440 " pdb=" ND2 ASN L 91 " model vdw 2.324 2.520 nonbonded pdb=" O ALA A 475 " pdb=" ND2 ASN A 487 " model vdw 2.382 2.520 nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.394 2.440 ... (remaining 22448 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 17 5.16 5 C 2030 2.51 5 N 528 2.21 5 O 617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 5.460 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 13.770 Find NCS groups from input model: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 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 : 0.003 0.031 3276 Z= 0.163 Angle : 0.790 10.631 4457 Z= 0.432 Chirality : 0.047 0.184 480 Planarity : 0.006 0.062 572 Dihedral : 13.114 88.529 1161 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.30 (0.38), residues: 400 helix: -3.71 (0.45), residues: 32 sheet: 2.48 (0.49), residues: 100 loop : -2.02 (0.31), residues: 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1604 time to fit residues: 11.7093 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5896 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3276 Z= 0.220 Angle : 0.740 8.255 4457 Z= 0.404 Chirality : 0.048 0.316 480 Planarity : 0.005 0.056 572 Dihedral : 7.949 26.981 456 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.31 (0.38), residues: 400 helix: -2.52 (0.84), residues: 26 sheet: 1.49 (0.46), residues: 113 loop : -1.94 (0.33), residues: 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.384 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.1485 time to fit residues: 10.3447 Evaluate side-chains 54 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0397 time to fit residues: 0.8156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3276 Z= 0.181 Angle : 0.661 8.417 4457 Z= 0.362 Chirality : 0.045 0.242 480 Planarity : 0.005 0.051 572 Dihedral : 7.137 28.169 456 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.35 (0.39), residues: 400 helix: -1.85 (1.05), residues: 27 sheet: 0.95 (0.44), residues: 113 loop : -1.77 (0.36), residues: 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.320 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 0.1672 time to fit residues: 11.3955 Evaluate side-chains 48 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0335 time to fit residues: 0.6383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 0.0000 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 33 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN A 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5817 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3276 Z= 0.155 Angle : 0.622 8.395 4457 Z= 0.338 Chirality : 0.043 0.191 480 Planarity : 0.005 0.049 572 Dihedral : 6.589 28.178 456 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.52 (0.39), residues: 400 helix: -1.90 (1.02), residues: 27 sheet: 0.60 (0.43), residues: 115 loop : -1.79 (0.35), residues: 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.366 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 0.1711 time to fit residues: 10.0393 Evaluate side-chains 46 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0611 time to fit residues: 0.5919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3276 Z= 0.220 Angle : 0.667 8.673 4457 Z= 0.364 Chirality : 0.045 0.264 480 Planarity : 0.005 0.049 572 Dihedral : 6.698 28.230 456 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.76 (0.39), residues: 400 helix: -2.16 (0.98), residues: 27 sheet: 0.31 (0.44), residues: 113 loop : -1.86 (0.35), residues: 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.356 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.1685 time to fit residues: 11.0921 Evaluate side-chains 50 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0333 time to fit residues: 0.6210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3276 Z= 0.214 Angle : 0.673 8.532 4457 Z= 0.363 Chirality : 0.045 0.245 480 Planarity : 0.005 0.051 572 Dihedral : 6.647 28.476 456 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.90 (0.39), residues: 400 helix: -2.14 (0.99), residues: 27 sheet: 0.12 (0.49), residues: 107 loop : -1.88 (0.35), residues: 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.324 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2016 time to fit residues: 11.3894 Evaluate side-chains 46 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0306 time to fit residues: 0.5183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3276 Z= 0.217 Angle : 0.680 8.547 4457 Z= 0.365 Chirality : 0.045 0.215 480 Planarity : 0.005 0.049 572 Dihedral : 6.585 28.308 456 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.00 (0.39), residues: 400 helix: -2.14 (0.98), residues: 27 sheet: 0.01 (0.49), residues: 108 loop : -1.94 (0.35), residues: 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.316 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.1793 time to fit residues: 10.9949 Evaluate side-chains 50 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0399 time to fit residues: 0.7336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3276 Z= 0.232 Angle : 0.700 8.498 4457 Z= 0.377 Chirality : 0.045 0.231 480 Planarity : 0.005 0.049 572 Dihedral : 6.573 28.089 456 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.12 (0.40), residues: 400 helix: -2.09 (0.99), residues: 27 sheet: -0.18 (0.50), residues: 108 loop : -1.98 (0.35), residues: 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.325 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1743 time to fit residues: 9.3761 Evaluate side-chains 43 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0338 time to fit residues: 0.5871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.0170 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3276 Z= 0.210 Angle : 0.680 8.246 4457 Z= 0.364 Chirality : 0.045 0.198 480 Planarity : 0.005 0.048 572 Dihedral : 6.413 28.135 456 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.14 (0.40), residues: 400 helix: -1.97 (1.01), residues: 27 sheet: -0.36 (0.51), residues: 107 loop : -1.93 (0.35), residues: 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1852 time to fit residues: 9.4496 Evaluate side-chains 42 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3276 Z= 0.202 Angle : 0.679 8.407 4457 Z= 0.364 Chirality : 0.044 0.168 480 Planarity : 0.005 0.048 572 Dihedral : 6.254 27.482 456 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.07 (0.41), residues: 400 helix: -1.86 (1.03), residues: 27 sheet: -0.29 (0.51), residues: 109 loop : -1.91 (0.36), residues: 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1616 time to fit residues: 8.1244 Evaluate side-chains 40 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 22 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN H 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.193140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.172413 restraints weight = 5128.165| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.68 r_work: 0.4277 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3276 Z= 0.171 Angle : 0.651 8.287 4457 Z= 0.346 Chirality : 0.043 0.148 480 Planarity : 0.004 0.046 572 Dihedral : 5.949 26.743 456 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.02 (0.40), residues: 400 helix: -1.88 (1.02), residues: 27 sheet: -0.23 (0.50), residues: 111 loop : -1.90 (0.36), residues: 262 =============================================================================== Job complete usr+sys time: 1210.17 seconds wall clock time: 22 minutes 31.34 seconds (1351.34 seconds total)