Starting phenix.real_space_refine (version: dev) on Fri Feb 17 07:38:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/02_2023/7mkm_23899.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/02_2023/7mkm_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_23899/02_2023/7mkm_23899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/02_2023/7mkm_23899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/02_2023/7mkm_23899.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkm_23899/02_2023/7mkm_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 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-4877/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: 2.44, per 1000 atoms: 0.76 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: 1.20 Conformation dependent library (CDL) restraints added in 465.3 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: 0.20 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: 0.71 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 6.160 Check model and map are aligned: 0.040 Process input model: 13.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- 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 : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1733 time to fit residues: 12.5804 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4440 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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: 0.5915 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3276 Z= 0.239 Angle : 0.749 8.279 4457 Z= 0.409 Chirality : 0.049 0.341 480 Planarity : 0.005 0.055 572 Dihedral : 7.992 26.968 456 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: -1.36 (0.38), residues: 400 helix: -2.51 (0.85), residues: 26 sheet: 1.41 (0.46), residues: 113 loop : -1.96 (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 : 0.344 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.1603 time to fit residues: 11.0249 Evaluate side-chains 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0388 time to fit residues: 0.8192 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 chunk 9 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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: 0.5881 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3276 Z= 0.179 Angle : 0.663 8.377 4457 Z= 0.363 Chirality : 0.046 0.287 480 Planarity : 0.005 0.050 572 Dihedral : 7.155 28.236 456 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.40 (0.39), residues: 400 helix: -1.81 (1.08), residues: 26 sheet: 0.88 (0.44), residues: 113 loop : -1.80 (0.35), residues: 261 *********************** 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 58 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.378 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 0.1623 time to fit residues: 11.4361 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0528 time to fit residues: 0.6131 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 0.0470 chunk 16 optimal weight: 0.0980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.2819 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= 0.197 Angle : 0.654 8.536 4457 Z= 0.359 Chirality : 0.044 0.208 480 Planarity : 0.005 0.050 572 Dihedral : 6.840 28.234 456 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -1.62 (0.39), residues: 400 helix: -1.98 (1.03), residues: 27 sheet: 0.48 (0.44), residues: 113 loop : -1.82 (0.36), residues: 260 *********************** 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 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.320 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.1822 time to fit residues: 11.8609 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0614 time to fit residues: 0.5966 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** ** A 506 GLN ** 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: 0.5938 moved from start: 0.3155 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= 0.210 Angle : 0.656 8.560 4457 Z= 0.361 Chirality : 0.045 0.264 480 Planarity : 0.005 0.050 572 Dihedral : 6.728 28.795 456 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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: -1.88 (0.39), residues: 400 helix: -2.15 (1.00), residues: 27 sheet: 0.16 (0.46), residues: 108 loop : -1.88 (0.35), residues: 265 *********************** 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 60 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.377 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 58 average time/residue: 0.1833 time to fit residues: 12.7156 Evaluate side-chains 53 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0320 time to fit residues: 0.5810 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.0170 chunk 36 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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: 0.5901 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3276 Z= 0.170 Angle : 0.632 8.503 4457 Z= 0.341 Chirality : 0.044 0.210 480 Planarity : 0.004 0.048 572 Dihedral : 6.416 28.625 456 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -1.83 (0.39), residues: 400 helix: -2.06 (1.00), residues: 27 sheet: 0.11 (0.48), residues: 107 loop : -1.80 (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 50 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.374 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1781 time to fit residues: 10.9376 Evaluate side-chains 49 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0352 time to fit residues: 0.5757 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.0670 chunk 18 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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: 0.5938 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3276 Z= 0.199 Angle : 0.655 8.650 4457 Z= 0.355 Chirality : 0.044 0.229 480 Planarity : 0.005 0.047 572 Dihedral : 6.390 28.210 456 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -1.90 (0.39), residues: 400 helix: -2.19 (0.98), residues: 27 sheet: 0.11 (0.49), residues: 108 loop : -1.88 (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: 2 poor density : 50 time to evaluate : 0.344 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.2073 time to fit residues: 12.7294 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0470 time to fit residues: 0.5753 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 32 optimal weight: 0.0060 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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: 0.5915 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3276 Z= 0.171 Angle : 0.641 8.500 4457 Z= 0.344 Chirality : 0.044 0.185 480 Planarity : 0.004 0.046 572 Dihedral : 6.229 27.951 456 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.86 % 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: -1.95 (0.39), residues: 400 helix: -2.12 (0.99), residues: 27 sheet: -0.07 (0.48), residues: 110 loop : -1.85 (0.35), residues: 263 *********************** 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 55 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.407 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.1749 time to fit residues: 11.7260 Evaluate side-chains 50 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0350 time to fit residues: 0.6201 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 22 optimal weight: 0.0980 chunk 17 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 0.0870 chunk 30 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 overall best weight: 0.2076 ------------------------------------------------------------------------------- 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: 0.5874 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3276 Z= 0.156 Angle : 0.627 8.412 4457 Z= 0.336 Chirality : 0.043 0.148 480 Planarity : 0.004 0.045 572 Dihedral : 5.966 27.649 456 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -1.89 (0.40), residues: 400 helix: -2.39 (0.84), residues: 33 sheet: 0.07 (0.49), residues: 110 loop : -1.80 (0.36), residues: 257 *********************** 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 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.358 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1743 time to fit residues: 10.8464 Evaluate side-chains 51 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5158 ------------------------------------------------------------------------------- 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: 0.0040 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 0.0170 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 overall best weight: 0.3030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3276 Z= 0.167 Angle : 0.633 8.558 4457 Z= 0.339 Chirality : 0.043 0.165 480 Planarity : 0.004 0.046 572 Dihedral : 5.953 27.041 456 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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: -1.95 (0.40), residues: 400 helix: -2.42 (0.84), residues: 33 sheet: -0.07 (0.50), residues: 110 loop : -1.79 (0.36), residues: 257 ********************** 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 48 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1792 time to fit residues: 10.4963 Evaluate side-chains 46 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5111 ------------------------------------------------------------------------------- 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: 0.8980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.0050 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.192637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.171265 restraints weight = 5161.722| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 2.85 r_work: 0.4257 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.4133 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= 0.202 Angle : 0.657 8.521 4457 Z= 0.354 Chirality : 0.044 0.171 480 Planarity : 0.005 0.047 572 Dihedral : 6.069 27.261 456 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -2.03 (0.40), residues: 400 helix: -2.44 (0.84), residues: 33 sheet: -0.18 (0.50), residues: 109 loop : -1.82 (0.36), residues: 258 =============================================================================== Job complete usr+sys time: 1246.07 seconds wall clock time: 23 minutes 17.95 seconds (1397.95 seconds total)