Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:18:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/04_2023/7x8w_33059_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/04_2023/7x8w_33059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/04_2023/7x8w_33059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/04_2023/7x8w_33059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/04_2023/7x8w_33059_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/04_2023/7x8w_33059_trim.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2186 2.51 5 N 574 2.21 5 O 682 1.98 5 H 3214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 28": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6674 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3065 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1883 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1627 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.33, per 1000 atoms: 0.50 Number of scatterers: 6674 At special positions: 0 Unit cell: (94.506, 63.004, 99.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 682 8.00 N 574 7.00 C 2186 6.00 H 3214 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN H 59 " Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 577.9 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.1% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.329A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.694A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.059A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.044A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 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 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.906A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.871A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.697A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.697A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 109 hydrogen bonds defined for protein. 258 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: 2.20 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3214 1.04 - 1.23: 82 1.23 - 1.43: 1488 1.43 - 1.62: 1954 1.62 - 1.82: 24 Bond restraints: 6762 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 MAN C 5 " pdb=" C2 MAN C 5 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" N GLN L 1 " pdb=" CA GLN L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N GLN L 1 " pdb=" H GLN L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 6757 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.81: 121 106.81 - 113.60: 7661 113.60 - 120.40: 2248 120.40 - 127.19: 2010 127.19 - 133.99: 40 Bond angle restraints: 12080 Sorted by residual: angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 106.35 6.60 3.00e+00 1.11e-01 4.85e+00 angle pdb=" C3 MAN C 5 " pdb=" C2 MAN C 5 " pdb=" O2 MAN C 5 " ideal model delta sigma weight residual 111.77 105.37 6.40 3.00e+00 1.11e-01 4.55e+00 angle pdb=" C3 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" O2 MAN C 4 " ideal model delta sigma weight residual 111.77 105.65 6.12 3.00e+00 1.11e-01 4.16e+00 angle pdb=" C4 FUC C 6 " pdb=" C3 FUC C 6 " pdb=" O3 FUC C 6 " ideal model delta sigma weight residual 113.24 107.38 5.86 3.00e+00 1.11e-01 3.82e+00 angle pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " pdb=" C5 BMA C 3 " ideal model delta sigma weight residual 118.82 113.51 5.31 3.00e+00 1.11e-01 3.14e+00 ... (remaining 12075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 2517 17.36 - 34.72: 159 34.72 - 52.08: 33 52.08 - 69.44: 3 69.44 - 86.80: 10 Dihedral angle restraints: 2722 sinusoidal: 1197 harmonic: 1525 Sorted by residual: dihedral pdb=" CB GLU L 52 " pdb=" CG GLU L 52 " pdb=" CD GLU L 52 " pdb=" OE1 GLU L 52 " ideal model delta sinusoidal sigma weight residual 0.00 86.80 -86.80 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CG ARG A 466 " pdb=" CD ARG A 466 " pdb=" NE ARG A 466 " pdb=" CZ ARG A 466 " ideal model delta sinusoidal sigma weight residual 90.00 132.13 -42.13 2 1.50e+01 4.44e-03 9.60e+00 dihedral pdb=" CA ALA A 348 " pdb=" C ALA A 348 " pdb=" N SER A 349 " pdb=" CA SER A 349 " ideal model delta harmonic sigma weight residual 180.00 164.52 15.48 0 5.00e+00 4.00e-02 9.59e+00 ... (remaining 2719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 459 0.055 - 0.110: 68 0.110 - 0.164: 12 0.164 - 0.219: 0 0.219 - 0.273: 2 Chirality restraints: 541 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN H 59 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 538 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 106 " -0.128 9.50e-02 1.11e+02 4.30e-02 2.23e+00 pdb=" NE ARG H 106 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 106 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 106 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG H 106 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 106 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 521 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 400 " -0.004 2.00e-02 2.50e+03 7.44e-03 5.54e-01 pdb=" C PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" O PHE A 400 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL A 401 " -0.004 2.00e-02 2.50e+03 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 616 2.22 - 2.81: 13564 2.81 - 3.41: 16199 3.41 - 4.00: 23473 4.00 - 4.60: 35091 Nonbonded interactions: 88943 Sorted by model distance: nonbonded pdb=" O GLY H 31 " pdb=" H SER H 103 " model vdw 1.624 1.850 nonbonded pdb=" O THR A 345 " pdb="HH22 ARG A 509 " model vdw 1.651 1.850 nonbonded pdb=" OD1 ASN A 360 " pdb=" HG1 THR A 523 " model vdw 1.655 1.850 nonbonded pdb="HH21 ARG A 454 " pdb=" O ASP A 467 " model vdw 1.674 1.850 nonbonded pdb="HH11 ARG A 457 " pdb=" O SER A 459 " model vdw 1.704 1.850 ... (remaining 88938 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 1.440 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.810 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 0.004 0.041 3548 Z= 0.264 Angle : 0.601 6.605 4825 Z= 0.280 Chirality : 0.045 0.273 541 Planarity : 0.004 0.056 611 Dihedral : 14.370 86.797 1218 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.40), residues: 429 helix: -3.61 (0.73), residues: 27 sheet: 0.25 (0.44), residues: 146 loop : -1.32 (0.38), residues: 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.4734 time to fit residues: 37.5951 Evaluate side-chains 58 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 3548 Z= 0.157 Angle : 0.491 5.179 4825 Z= 0.244 Chirality : 0.041 0.149 541 Planarity : 0.003 0.036 611 Dihedral : 3.680 16.535 479 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.40), residues: 429 helix: -3.83 (0.66), residues: 32 sheet: 0.48 (0.45), residues: 136 loop : -1.25 (0.38), residues: 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4650 time to fit residues: 32.4672 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0772 time to fit residues: 0.7831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3548 Z= 0.149 Angle : 0.480 6.314 4825 Z= 0.235 Chirality : 0.040 0.154 541 Planarity : 0.003 0.042 611 Dihedral : 3.572 15.135 479 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.66 % Favored : 95.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.40), residues: 429 helix: -3.73 (0.71), residues: 32 sheet: 0.44 (0.45), residues: 142 loop : -1.23 (0.38), residues: 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.4623 time to fit residues: 31.5907 Evaluate side-chains 58 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3548 Z= 0.262 Angle : 0.498 6.544 4825 Z= 0.245 Chirality : 0.040 0.148 541 Planarity : 0.003 0.040 611 Dihedral : 3.668 14.550 479 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.83 % Favored : 93.94 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.40), residues: 429 helix: -3.75 (0.71), residues: 32 sheet: 0.37 (0.45), residues: 142 loop : -1.30 (0.38), residues: 255 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4713 time to fit residues: 32.8465 Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0851 time to fit residues: 0.8946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.0020 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 3548 Z= 0.156 Angle : 0.481 6.554 4825 Z= 0.237 Chirality : 0.040 0.145 541 Planarity : 0.003 0.045 611 Dihedral : 3.585 15.214 479 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.43 % Favored : 95.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.41), residues: 429 helix: -3.74 (0.70), residues: 32 sheet: 0.39 (0.45), residues: 142 loop : -1.22 (0.38), residues: 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.4609 time to fit residues: 33.0177 Evaluate side-chains 58 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3548 Z= 0.226 Angle : 0.489 5.956 4825 Z= 0.242 Chirality : 0.040 0.147 541 Planarity : 0.003 0.050 611 Dihedral : 3.643 14.691 479 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.13 % Favored : 94.64 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.41), residues: 429 helix: -3.74 (0.70), residues: 32 sheet: 0.34 (0.45), residues: 142 loop : -1.27 (0.38), residues: 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.4406 time to fit residues: 31.9461 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.604 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0822 time to fit residues: 0.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3548 Z= 0.132 Angle : 0.473 5.466 4825 Z= 0.234 Chirality : 0.040 0.140 541 Planarity : 0.003 0.051 611 Dihedral : 3.532 15.596 479 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.66 % Favored : 95.10 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.41), residues: 429 helix: -3.72 (0.70), residues: 32 sheet: 0.43 (0.45), residues: 142 loop : -1.15 (0.39), residues: 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.4534 time to fit residues: 33.8012 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.0770 chunk 31 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 3548 Z= 0.125 Angle : 0.467 4.850 4825 Z= 0.231 Chirality : 0.040 0.151 541 Planarity : 0.003 0.054 611 Dihedral : 3.472 15.480 479 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.41), residues: 429 helix: -3.67 (0.72), residues: 32 sheet: 0.39 (0.45), residues: 142 loop : -1.12 (0.39), residues: 255 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.4513 time to fit residues: 31.6188 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0842 time to fit residues: 0.8513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3548 Z= 0.148 Angle : 0.469 4.616 4825 Z= 0.232 Chirality : 0.040 0.151 541 Planarity : 0.003 0.056 611 Dihedral : 3.471 15.213 479 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.66 % Favored : 95.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.41), residues: 429 helix: -3.63 (0.73), residues: 32 sheet: 0.42 (0.45), residues: 142 loop : -1.15 (0.39), residues: 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.4665 time to fit residues: 32.6834 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 3548 Z= 0.121 Angle : 0.462 3.966 4825 Z= 0.229 Chirality : 0.040 0.150 541 Planarity : 0.003 0.059 611 Dihedral : 3.395 15.419 479 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.96 % Favored : 95.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.41), residues: 429 helix: -3.63 (0.73), residues: 32 sheet: 0.51 (0.45), residues: 142 loop : -1.07 (0.39), residues: 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.4609 time to fit residues: 32.2490 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.088129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.070892 restraints weight = 18238.434| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.36 r_work: 0.2781 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3548 Z= 0.134 Angle : 0.460 3.656 4825 Z= 0.229 Chirality : 0.040 0.154 541 Planarity : 0.004 0.065 611 Dihedral : 3.405 14.991 479 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.41), residues: 429 helix: -3.63 (0.73), residues: 32 sheet: 0.51 (0.45), residues: 142 loop : -1.10 (0.39), residues: 255 =============================================================================== Job complete usr+sys time: 2538.64 seconds wall clock time: 45 minutes 6.31 seconds (2706.31 seconds total)