Starting phenix.real_space_refine (version: dev) on Sat Feb 18 01:22:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2023/7x8w_33059_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_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_33059/02_2023/7x8w_33059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2023/7x8w_33059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2023/7x8w_33059_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_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 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-dev-4877/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 dihedrals: 4 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.63, per 1000 atoms: 0.54 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: 5.66 Conformation dependent library (CDL) restraints added in 594.2 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: 0.24 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: 2.06 Time building geometry restraints manager: 5.78 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=" 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 bond pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" CB TRP H 50 " pdb=" CG TRP H 50 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.01e+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=" N GLY H 49 " pdb=" CA GLY H 49 " pdb=" C GLY H 49 " ideal model delta sigma weight residual 110.66 113.55 -2.89 1.90e+00 2.77e-01 2.31e+00 angle pdb=" CA GLN L 1 " pdb=" N GLN L 1 " pdb=" H GLN L 1 " ideal model delta sigma weight residual 114.00 109.44 4.56 3.00e+00 1.11e-01 2.31e+00 angle pdb=" CA GLN H 1 " pdb=" N GLN H 1 " pdb=" H GLN H 1 " ideal model delta sigma weight residual 114.00 109.47 4.53 3.00e+00 1.11e-01 2.28e+00 angle pdb=" C PHE A 400 " pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " ideal model delta sigma weight residual 110.45 107.51 2.94 2.15e+00 2.16e-01 1.87e+00 angle pdb=" N VAL L 35 " pdb=" CA VAL L 35 " pdb=" C VAL L 35 " ideal model delta sigma weight residual 109.34 106.67 2.67 2.08e+00 2.31e-01 1.65e+00 ... (remaining 12075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 2580 17.36 - 34.72: 159 34.72 - 52.08: 33 52.08 - 69.44: 3 69.44 - 86.80: 10 Dihedral angle restraints: 2785 sinusoidal: 1260 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 2782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 449 0.047 - 0.094: 63 0.094 - 0.141: 28 0.141 - 0.188: 0 0.188 - 0.234: 1 Chirality restraints: 541 Sorted by residual: 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 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-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 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. 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 1.590 Check model and map are aligned: 0.100 Process input model: 24.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 0.033 3548 Z= 0.224 Angle : 0.496 3.757 4825 Z= 0.258 Chirality : 0.041 0.234 541 Planarity : 0.004 0.056 611 Dihedral : 14.069 86.797 1281 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 : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.4604 time to fit residues: 36.7177 Evaluate side-chains 58 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5806 ------------------------------------------------------------------------------- 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: 0.8456 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3548 Z= 0.165 Angle : 0.482 5.199 4825 Z= 0.243 Chirality : 0.041 0.209 541 Planarity : 0.003 0.034 611 Dihedral : 3.972 17.895 542 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % 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: -1.30 (0.40), residues: 429 helix: -3.81 (0.67), residues: 32 sheet: 0.47 (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 : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4577 time to fit residues: 31.8163 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0823 time to fit residues: 0.7439 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3548 Z= 0.271 Angle : 0.497 6.429 4825 Z= 0.249 Chirality : 0.041 0.214 541 Planarity : 0.003 0.040 611 Dihedral : 4.064 18.999 542 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.29 % Favored : 93.47 % 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: -1.41 (0.40), residues: 429 helix: -3.76 (0.70), residues: 32 sheet: 0.33 (0.45), residues: 142 loop : -1.33 (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 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.4744 time to fit residues: 33.0488 Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6355 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.0843 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= 0.150 Angle : 0.475 6.631 4825 Z= 0.237 Chirality : 0.041 0.196 541 Planarity : 0.003 0.039 611 Dihedral : 3.950 20.053 542 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.91 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: -1.33 (0.40), residues: 429 helix: -3.77 (0.70), residues: 32 sheet: 0.39 (0.45), residues: 142 loop : -1.27 (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 : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4723 time to fit residues: 32.8804 Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0830 time to fit residues: 0.8654 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.8476 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3548 Z= 0.217 Angle : 0.481 6.343 4825 Z= 0.240 Chirality : 0.041 0.196 541 Planarity : 0.003 0.046 611 Dihedral : 3.974 20.763 542 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.06 % Favored : 93.71 % 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: -3.74 (0.70), residues: 32 sheet: 0.37 (0.45), residues: 142 loop : -1.29 (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 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.4666 time to fit residues: 34.1768 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7657 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3548 Z= 0.209 Angle : 0.478 5.977 4825 Z= 0.239 Chirality : 0.041 0.175 541 Planarity : 0.003 0.049 611 Dihedral : 3.974 21.877 542 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.66 % Favored : 95.10 % 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: -1.33 (0.40), residues: 429 helix: -3.74 (0.71), residues: 32 sheet: 0.36 (0.45), residues: 142 loop : -1.26 (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 66 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.4341 time to fit residues: 32.6508 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0877 time to fit residues: 0.8185 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8458 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3548 Z= 0.139 Angle : 0.462 5.625 4825 Z= 0.232 Chirality : 0.041 0.179 541 Planarity : 0.003 0.051 611 Dihedral : 3.889 22.701 542 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.90 % Favored : 94.87 % 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: -1.24 (0.41), residues: 429 helix: -3.70 (0.71), residues: 32 sheet: 0.39 (0.45), residues: 142 loop : -1.17 (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 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.4850 time to fit residues: 34.9654 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6013 ------------------------------------------------------------------------------- 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: 0.8980 chunk 31 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.0040 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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: 0.8446 moved from start: 0.1261 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= 0.132 Angle : 0.462 4.951 4825 Z= 0.230 Chirality : 0.040 0.179 541 Planarity : 0.003 0.054 611 Dihedral : 3.826 23.463 542 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.77 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: -1.18 (0.41), residues: 429 helix: -3.64 (0.73), residues: 32 sheet: 0.42 (0.45), residues: 142 loop : -1.13 (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 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.4520 time to fit residues: 33.1680 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.576 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0868 time to fit residues: 0.8348 ------------------------------------------------------------------------------- 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: 0.0670 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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: 0.8442 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3548 Z= 0.132 Angle : 0.456 4.542 4825 Z= 0.228 Chirality : 0.040 0.180 541 Planarity : 0.003 0.056 611 Dihedral : 3.798 23.765 542 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.43 % Favored : 95.34 % 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: -1.16 (0.41), residues: 429 helix: -3.63 (0.73), residues: 32 sheet: 0.42 (0.45), residues: 142 loop : -1.10 (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 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4512 time to fit residues: 31.9301 Evaluate side-chains 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1348 time to fit residues: 0.9089 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8450 moved from start: 0.1364 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= 0.154 Angle : 0.457 4.011 4825 Z= 0.230 Chirality : 0.040 0.184 541 Planarity : 0.003 0.058 611 Dihedral : 3.811 23.940 542 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % 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: -1.18 (0.41), residues: 429 helix: -3.63 (0.73), residues: 32 sheet: 0.42 (0.45), residues: 142 loop : -1.13 (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 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.4642 time to fit residues: 31.9667 Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6960 ------------------------------------------------------------------------------- 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: 0.2980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.088243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.070838 restraints weight = 18305.824| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.41 r_work: 0.2779 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1403 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= 0.135 Angle : 0.452 3.812 4825 Z= 0.227 Chirality : 0.040 0.180 541 Planarity : 0.003 0.058 611 Dihedral : 3.769 24.317 542 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -1.13 (0.41), residues: 429 helix: -3.61 (0.74), residues: 32 sheet: 0.47 (0.45), residues: 142 loop : -1.10 (0.39), residues: 255 =============================================================================== Job complete usr+sys time: 2513.44 seconds wall clock time: 45 minutes 4.64 seconds (2704.64 seconds total)