Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 21:40:33 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2021/7kxy_23067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2021/7kxy_23067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2021/7kxy_23067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2021/7kxy_23067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2021/7kxy_23067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kxy_23067/12_2021/7kxy_23067.pdb" } resolution = 4.4 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 1989": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 9510 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4704 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 30, 'TRANS': 557} Chain breaks: 8 Chain: "B" Number of atoms: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4806 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'CIS': 1, 'TRANS': 564} Chain breaks: 4 Time building chain proxies: 5.47, per 1000 atoms: 0.58 Number of scatterers: 9510 At special positions: 0 Unit cell: (85.8, 96.8, 134.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1784 8.00 N 1630 7.00 C 6048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS B1697 " - pdb=" SG CYS B1723 " distance=2.03 Simple disulfide: pdb=" SG CYS B1879 " - pdb=" SG CYS B2033 " distance=2.03 Simple disulfide: pdb=" SG CYS B2038 " - pdb=" SG CYS B2193 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.5 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 12 sheets defined 2.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 640 through 645 removed outlier: 4.331A pdb=" N LYS A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 1779 through 1783 removed outlier: 3.698A pdb=" N MET B1783 " --> pdb=" O ILE B1780 " (cutoff:3.500A) Processing helix chain 'B' and resid 1861 through 1866 removed outlier: 3.506A pdb=" N GLN B1864 " --> pdb=" O GLY B1861 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B1865 " --> pdb=" O GLU B1862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.980A pdb=" N ALA A 9 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.969A pdb=" N LEU A 62 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N CYS A 165 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ALA A 64 " --> pdb=" O CYS A 165 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 164 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 231 removed outlier: 3.584A pdb=" N ILE A 225 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 268 " --> pdb=" O TRP A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 334 removed outlier: 3.869A pdb=" N VAL A 331 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.741A pdb=" N LEU A 494 " --> pdb=" O ILE A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 594 through 595 removed outlier: 3.585A pdb=" N LEU A 594 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1555 through 1556 Processing sheet with id=AA8, first strand: chain 'B' and resid 1620 through 1622 removed outlier: 3.506A pdb=" N LEU B1721 " --> pdb=" O ILE B1620 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B1622 " --> pdb=" O LEU B1721 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1800 through 1801 Processing sheet with id=AB1, first strand: chain 'B' and resid 1814 through 1816 removed outlier: 3.744A pdb=" N HIS B1815 " --> pdb=" O ASN B1857 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B1857 " --> pdb=" O HIS B1815 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1896 through 1897 removed outlier: 4.499A pdb=" N LYS B1896 " --> pdb=" O GLN B1936 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B1936 " --> pdb=" O LYS B1896 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 1977 through 1978 42 hydrogen bonds defined for protein. 90 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: 1.76 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3065 1.35 - 1.47: 2405 1.47 - 1.59: 4197 1.59 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 9746 Sorted by residual: bond pdb=" C ILE B2176 " pdb=" N PRO B2177 " ideal model delta sigma weight residual 1.335 1.356 -0.021 8.70e-03 1.32e+04 5.81e+00 bond pdb=" CA THR B2018 " pdb=" C THR B2018 " ideal model delta sigma weight residual 1.517 1.528 -0.011 6.30e-03 2.52e+04 3.00e+00 bond pdb=" CA ARG B2074 " pdb=" CB ARG B2074 " ideal model delta sigma weight residual 1.528 1.557 -0.029 1.67e-02 3.59e+03 2.95e+00 bond pdb=" C GLU A 42 " pdb=" N PRO A 43 " ideal model delta sigma weight residual 1.332 1.352 -0.020 1.33e-02 5.65e+03 2.32e+00 bond pdb=" CA PHE B1872 " pdb=" CB PHE B1872 " ideal model delta sigma weight residual 1.526 1.549 -0.022 1.53e-02 4.27e+03 2.16e+00 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.47: 321 106.47 - 113.37: 5167 113.37 - 120.26: 3342 120.26 - 127.16: 4215 127.16 - 134.06: 139 Bond angle restraints: 13184 Sorted by residual: angle pdb=" CA THR B2018 " pdb=" C THR B2018 " pdb=" N ARG B2019 " ideal model delta sigma weight residual 119.46 116.96 2.50 6.10e-01 2.69e+00 1.68e+01 angle pdb=" C SER A 262 " pdb=" N ALA A 263 " pdb=" CA ALA A 263 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N ILE A 390 " pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 112.17 108.72 3.45 9.50e-01 1.11e+00 1.32e+01 angle pdb=" C TYR B1678 " pdb=" CA TYR B1678 " pdb=" CB TYR B1678 " ideal model delta sigma weight residual 114.40 109.96 4.44 1.25e+00 6.40e-01 1.26e+01 angle pdb=" CA ARG A 445 " pdb=" C ARG A 445 " pdb=" N ALA A 446 " ideal model delta sigma weight residual 118.27 123.71 -5.44 1.59e+00 3.96e-01 1.17e+01 ... (remaining 13179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5171 17.54 - 35.07: 505 35.07 - 52.61: 112 52.61 - 70.15: 24 70.15 - 87.68: 11 Dihedral angle restraints: 5823 sinusoidal: 2392 harmonic: 3431 Sorted by residual: dihedral pdb=" CA VAL A 565 " pdb=" C VAL A 565 " pdb=" N PRO A 566 " pdb=" CA PRO A 566 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA TYR A 415 " pdb=" C TYR A 415 " pdb=" N SER A 416 " pdb=" CA SER A 416 " ideal model delta harmonic sigma weight residual 180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LEU A 403 " pdb=" C LEU A 403 " pdb=" N LYS A 404 " pdb=" CA LYS A 404 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 5820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 777 0.030 - 0.060: 368 0.060 - 0.090: 165 0.090 - 0.120: 73 0.120 - 0.150: 20 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA ILE B2169 " pdb=" N ILE B2169 " pdb=" C ILE B2169 " pdb=" CB ILE B2169 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE B1890 " pdb=" N ILE B1890 " pdb=" C ILE B1890 " pdb=" CB ILE B1890 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1400 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 565 " 0.048 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO A 566 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 160 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO A 161 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 136 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 137 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " 0.030 5.00e-02 4.00e+02 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 861 2.74 - 3.28: 9626 3.28 - 3.82: 15522 3.82 - 4.36: 18165 4.36 - 4.90: 29045 Nonbonded interactions: 73219 Sorted by model distance: nonbonded pdb=" OG SER B1648 " pdb=" OG1 THR B1685 " model vdw 2.197 2.440 nonbonded pdb=" O ARG B1910 " pdb=" NH1 ARG B2027 " model vdw 2.236 2.520 nonbonded pdb=" O LYS A 607 " pdb=" OG SER B1692 " model vdw 2.260 2.440 nonbonded pdb=" O VAL B1624 " pdb=" NZ LYS B1725 " model vdw 2.276 2.520 nonbonded pdb=" OG1 THR B1962 " pdb=" O THR B2025 " model vdw 2.277 2.440 ... (remaining 73214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6048 2.51 5 N 1630 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.200 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 25.520 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 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 0.069 9746 Z= 0.237 Angle : 0.822 8.939 13184 Z= 0.472 Chirality : 0.046 0.150 1403 Planarity : 0.005 0.071 1689 Dihedral : 15.126 87.683 3599 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 4.16 % Allowed : 26.02 % Favored : 69.82 % Rotamer Outliers : 7.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -5.90 (0.19), residues: 1153 helix: -5.24 (0.21), residues: 25 sheet: -4.15 (0.32), residues: 174 loop : -4.26 (0.16), residues: 954 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 188 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 21 residues processed: 243 average time/residue: 0.2009 time to fit residues: 68.9222 Evaluate side-chains 152 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1125 time to fit residues: 5.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 211 ASN A 293 GLN A 362 HIS A 448 GLN A 468 ASN A 581 GLN A 597 HIS B1547 ASN B1670 ASN B1778 HIS ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1982 ASN B1986 ASN B1991 ASN B2051 ASN B2078 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9746 Z= 0.191 Angle : 0.741 8.827 13184 Z= 0.374 Chirality : 0.049 0.191 1403 Planarity : 0.005 0.061 1689 Dihedral : 7.025 30.439 1282 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 15.09 % Favored : 84.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.41 (0.20), residues: 1153 helix: -4.55 (0.62), residues: 24 sheet: -3.94 (0.31), residues: 207 loop : -3.84 (0.17), residues: 922 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2282 time to fit residues: 55.4377 Evaluate side-chains 125 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 541 ASN ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1713 HIS ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9746 Z= 0.277 Angle : 0.799 9.134 13184 Z= 0.406 Chirality : 0.049 0.220 1403 Planarity : 0.007 0.102 1689 Dihedral : 7.353 28.478 1282 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 29.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 22.03 % Favored : 77.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -5.35 (0.21), residues: 1153 helix: -4.94 (0.43), residues: 32 sheet: -3.93 (0.31), residues: 225 loop : -3.72 (0.18), residues: 896 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2250 time to fit residues: 46.7057 Evaluate side-chains 124 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.148 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1553 ASN ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1973 GLN ** B1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9746 Z= 0.247 Angle : 0.783 9.395 13184 Z= 0.396 Chirality : 0.050 0.205 1403 Planarity : 0.006 0.101 1689 Dihedral : 7.353 33.001 1282 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 29.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.99 % Favored : 80.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.24 (0.21), residues: 1153 helix: -4.83 (0.49), residues: 32 sheet: -3.95 (0.31), residues: 224 loop : -3.62 (0.18), residues: 897 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2220 time to fit residues: 48.1658 Evaluate side-chains 123 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1986 ASN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9746 Z= 0.206 Angle : 0.746 9.647 13184 Z= 0.373 Chirality : 0.048 0.213 1403 Planarity : 0.006 0.094 1689 Dihedral : 6.939 34.091 1282 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 25.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.47 % Favored : 81.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.07 (0.21), residues: 1153 helix: -4.81 (0.45), residues: 32 sheet: -3.96 (0.34), residues: 195 loop : -3.50 (0.18), residues: 926 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2246 time to fit residues: 48.7367 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 9746 Z= 0.422 Angle : 0.967 10.778 13184 Z= 0.493 Chirality : 0.054 0.291 1403 Planarity : 0.008 0.104 1689 Dihedral : 8.380 31.559 1282 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 40.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 24.98 % Favored : 74.85 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % Twisted General : 0.18 % 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: -5.55 (0.20), residues: 1153 helix: -4.75 (0.45), residues: 33 sheet: -4.21 (0.32), residues: 191 loop : -3.89 (0.17), residues: 929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2100 time to fit residues: 41.2670 Evaluate side-chains 113 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1547 ASN ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1864 GLN B2085 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 9746 Z= 0.337 Angle : 0.895 10.921 13184 Z= 0.452 Chirality : 0.052 0.261 1403 Planarity : 0.007 0.097 1689 Dihedral : 8.117 32.716 1282 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 35.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 22.81 % Favored : 77.10 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -5.54 (0.20), residues: 1153 helix: -4.77 (0.47), residues: 33 sheet: -4.15 (0.32), residues: 191 loop : -3.90 (0.17), residues: 929 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.2098 time to fit residues: 42.6274 Evaluate side-chains 114 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9746 Z= 0.201 Angle : 0.777 9.826 13184 Z= 0.387 Chirality : 0.049 0.297 1403 Planarity : 0.006 0.096 1689 Dihedral : 7.143 33.480 1282 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.22 % Favored : 83.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.13 (0.21), residues: 1153 helix: -4.73 (0.46), residues: 31 sheet: -3.78 (0.33), residues: 203 loop : -3.60 (0.18), residues: 919 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2068 time to fit residues: 45.5212 Evaluate side-chains 119 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 9746 Z= 0.322 Angle : 0.875 10.064 13184 Z= 0.441 Chirality : 0.053 0.293 1403 Planarity : 0.007 0.099 1689 Dihedral : 7.836 33.678 1282 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 33.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 23.24 % Favored : 76.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % Twisted General : 0.09 % 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: -5.29 (0.21), residues: 1153 helix: -4.61 (0.54), residues: 32 sheet: -4.09 (0.31), residues: 199 loop : -3.67 (0.18), residues: 922 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2072 time to fit residues: 43.0679 Evaluate side-chains 122 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1683 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 9746 Z= 0.264 Angle : 0.841 10.061 13184 Z= 0.421 Chirality : 0.052 0.270 1403 Planarity : 0.007 0.118 1689 Dihedral : 7.641 33.030 1282 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 31.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 20.03 % Favored : 79.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % Twisted General : 0.09 % 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: -5.13 (0.21), residues: 1153 helix: -4.33 (0.68), residues: 26 sheet: -3.94 (0.34), residues: 188 loop : -3.60 (0.18), residues: 939 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1916 time to fit residues: 40.8618 Evaluate side-chains 118 residues out of total 1045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.170 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2078 GLN ** B2085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.160109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.149479 restraints weight = 28258.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.151419 restraints weight = 18877.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.152647 restraints weight = 13583.679| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 9746 Z= 0.220 Angle : 0.784 12.160 13184 Z= 0.390 Chirality : 0.050 0.254 1403 Planarity : 0.006 0.094 1689 Dihedral : 7.168 33.652 1282 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.91 % Favored : 81.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.75 % Twisted General : 0.09 % 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: -4.97 (0.22), residues: 1153 helix: -4.40 (0.58), residues: 32 sheet: -3.77 (0.35), residues: 178 loop : -3.50 (0.18), residues: 943 =============================================================================== Job complete usr+sys time: 1828.45 seconds wall clock time: 35 minutes 44.85 seconds (2144.85 seconds total)