Starting phenix.real_space_refine on Wed Nov 15 00:41:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fas_31505/11_2023/7fas_31505.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fas_31505/11_2023/7fas_31505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fas_31505/11_2023/7fas_31505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fas_31505/11_2023/7fas_31505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fas_31505/11_2023/7fas_31505.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fas_31505/11_2023/7fas_31505.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6414 2.51 5 N 1753 2.21 5 O 1931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ASP 594": "OD1" <-> "OD2" Residue "A GLU 1032": "OE1" <-> "OE2" Residue "A GLU 1143": "OE1" <-> "OE2" Residue "A GLU 1693": "OE1" <-> "OE2" Residue "A TYR 1862": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10173 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1229, 10173 Classifications: {'peptide': 1229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 31, 'TRANS': 1197} Chain breaks: 46 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.70, per 1000 atoms: 0.56 Number of scatterers: 10173 At special positions: 0 Unit cell: (109.62, 140.94, 103.356, 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 75 16.00 O 1931 8.00 N 1753 7.00 C 6414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 588 " - pdb=" SG CYS A 592 " distance=2.03 Simple disulfide: pdb=" SG CYS A 643 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 769 " - pdb=" SG CYS A 901 " distance=2.03 Simple disulfide: pdb=" SG CYS A 783 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 957 " distance=2.03 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1090 " distance=2.03 Simple disulfide: pdb=" SG CYS A1088 " - pdb=" SG CYS A1193 " distance=2.02 Simple disulfide: pdb=" SG CYS A1140 " - pdb=" SG CYS A1171 " distance=2.03 Simple disulfide: pdb=" SG CYS A1470 " - pdb=" SG CYS A1483 " distance=2.03 Simple disulfide: pdb=" SG CYS A1670 " - pdb=" SG CYS A1777 " distance=2.03 Simple disulfide: pdb=" SG CYS A1802 " - pdb=" SG CYS A1904 " distance=2.03 Simple disulfide: pdb=" SG CYS A1816 " - pdb=" SG CYS A1833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1837 " - pdb=" SG CYS A1955 " distance=2.39 Simple disulfide: pdb=" SG CYS A1891 " - pdb=" SG CYS A1902 " 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 Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 1 sheets defined 61.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 119 through 142 removed outlier: 3.979A pdb=" N PHE A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 167 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 208 through 226 removed outlier: 5.605A pdb=" N GLN A 219 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 226 " --> pdb=" O TRP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 273 through 299 removed outlier: 3.724A pdb=" N ARG A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.763A pdb=" N GLU A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 608 through 627 removed outlier: 3.556A pdb=" N ASN A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 641 through 658 Processing helix chain 'A' and resid 667 through 683 Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.752A pdb=" N ILE A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 755 through 781 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 801 through 813 removed outlier: 3.540A pdb=" N GLU A 806 " --> pdb=" O LYS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 847 Processing helix chain 'A' and resid 872 through 884 Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 943 through 945 No H-bonds generated for 'chain 'A' and resid 943 through 945' Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 1016 through 1043 removed outlier: 3.866A pdb=" N VAL A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1117 removed outlier: 3.608A pdb=" N ILE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1146 Processing helix chain 'A' and resid 1163 through 1171 Processing helix chain 'A' and resid 1180 through 1199 Processing helix chain 'A' and resid 1291 through 1306 removed outlier: 4.560A pdb=" N GLN A1296 " --> pdb=" O LYS A1292 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS A1306 " --> pdb=" O LEU A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1355 removed outlier: 4.299A pdb=" N ALA A1341 " --> pdb=" O GLY A1337 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A1355 " --> pdb=" O ASN A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1405 Processing helix chain 'A' and resid 1405 through 1419 Processing helix chain 'A' and resid 1444 through 1468 removed outlier: 3.552A pdb=" N LYS A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1512 removed outlier: 3.945A pdb=" N ARG A1485 " --> pdb=" O GLY A1481 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A1500 " --> pdb=" O GLU A1496 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A1503 " --> pdb=" O GLN A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1612 Processing helix chain 'A' and resid 1617 through 1624 removed outlier: 4.104A pdb=" N ILE A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A1622 " --> pdb=" O LEU A1618 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A1624 " --> pdb=" O PRO A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1657 Processing helix chain 'A' and resid 1662 through 1685 Processing helix chain 'A' and resid 1692 through 1706 removed outlier: 3.540A pdb=" N GLU A1704 " --> pdb=" O SER A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1726 removed outlier: 3.610A pdb=" N THR A1721 " --> pdb=" O LYS A1717 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP A1724 " --> pdb=" O ARG A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1762 Processing helix chain 'A' and resid 1788 through 1816 Processing helix chain 'A' and resid 1832 through 1859 removed outlier: 3.618A pdb=" N ALA A1836 " --> pdb=" O GLU A1832 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP A1843 " --> pdb=" O ASN A1839 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A1844 " --> pdb=" O TYR A1840 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN A1845 " --> pdb=" O THR A1841 " (cutoff:3.500A) Proline residue: A1846 - end of helix Processing helix chain 'A' and resid 1882 through 1888 Processing helix chain 'A' and resid 1952 through 1969 Processing helix chain 'A' and resid 1969 through 1974 Processing sheet with id=AA1, first strand: chain 'A' and resid 911 through 915 541 hydrogen bonds defined for protein. 1611 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: 2.78 Time building geometry restraints manager: 6.96 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: 3265 1.35 - 1.47: 2491 1.47 - 1.59: 4509 1.59 - 1.71: 0 1.71 - 1.83: 90 Bond restraints: 10355 Sorted by residual: bond pdb=" CA ARG A 848 " pdb=" C ARG A 848 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.38e-02 5.25e+03 1.89e+00 bond pdb=" C ILE A 900 " pdb=" O ILE A 900 " ideal model delta sigma weight residual 1.241 1.227 0.014 1.06e-02 8.90e+03 1.77e+00 bond pdb=" CB ASN A1898 " pdb=" CG ASN A1898 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.06e+00 bond pdb=" C PRO A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.326 1.339 -0.013 1.44e-02 4.82e+03 7.98e-01 bond pdb=" C ASP A1741 " pdb=" N PRO A1742 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.85e-01 ... (remaining 10350 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 203 107.15 - 113.87: 5733 113.87 - 120.60: 4248 120.60 - 127.32: 3566 127.32 - 134.04: 122 Bond angle restraints: 13872 Sorted by residual: angle pdb=" N LYS A1952 " pdb=" CA LYS A1952 " pdb=" C LYS A1952 " ideal model delta sigma weight residual 112.93 107.70 5.23 1.33e+00 5.65e-01 1.55e+01 angle pdb=" N ILE A1831 " pdb=" CA ILE A1831 " pdb=" C ILE A1831 " ideal model delta sigma weight residual 113.47 109.52 3.95 1.01e+00 9.80e-01 1.53e+01 angle pdb=" N ILE A 900 " pdb=" CA ILE A 900 " pdb=" C ILE A 900 " ideal model delta sigma weight residual 113.42 109.23 4.19 1.17e+00 7.31e-01 1.28e+01 angle pdb=" C LYS A1087 " pdb=" N CYS A1088 " pdb=" CA CYS A1088 " ideal model delta sigma weight residual 122.06 115.79 6.27 1.86e+00 2.89e-01 1.14e+01 angle pdb=" N CYS A 901 " pdb=" CA CYS A 901 " pdb=" C CYS A 901 " ideal model delta sigma weight residual 112.26 116.69 -4.43 1.32e+00 5.74e-01 1.13e+01 ... (remaining 13867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5490 17.88 - 35.76: 649 35.76 - 53.63: 136 53.63 - 71.51: 20 71.51 - 89.39: 10 Dihedral angle restraints: 6305 sinusoidal: 2710 harmonic: 3595 Sorted by residual: dihedral pdb=" CB CYS A 783 " pdb=" SG CYS A 783 " pdb=" SG CYS A 801 " pdb=" CB CYS A 801 " ideal model delta sinusoidal sigma weight residual 93.00 35.63 57.37 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CB CYS A1088 " pdb=" SG CYS A1088 " pdb=" SG CYS A1193 " pdb=" CB CYS A1193 " ideal model delta sinusoidal sigma weight residual -86.00 -138.45 52.45 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CB CYS A1670 " pdb=" SG CYS A1670 " pdb=" SG CYS A1777 " pdb=" CB CYS A1777 " ideal model delta sinusoidal sigma weight residual 93.00 128.25 -35.25 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 6302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 973 0.030 - 0.061: 325 0.061 - 0.091: 99 0.091 - 0.122: 39 0.122 - 0.152: 5 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA ILE A 900 " pdb=" N ILE A 900 " pdb=" C ILE A 900 " pdb=" CB ILE A 900 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA CYS A1088 " pdb=" N CYS A1088 " pdb=" C CYS A1088 " pdb=" CB CYS A1088 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA CYS A 901 " pdb=" N CYS A 901 " pdb=" C CYS A 901 " pdb=" CB CYS A 901 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1438 not shown) Planarity restraints: 1753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1619 " 0.060 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A1620 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A1620 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A1620 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 665 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ASN A 665 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN A 665 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 666 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1607 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A1608 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A1608 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1608 " -0.021 5.00e-02 4.00e+02 ... (remaining 1750 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 566 2.73 - 3.28: 10608 3.28 - 3.82: 16582 3.82 - 4.36: 18234 4.36 - 4.90: 31435 Nonbonded interactions: 77425 Sorted by model distance: nonbonded pdb=" NH1 ARG A1609 " pdb=" OD2 ASP A1679 " model vdw 2.193 2.520 nonbonded pdb=" O ASP A 169 " pdb=" NE2 GLN A 274 " model vdw 2.207 2.520 nonbonded pdb=" NH1 ARG A 772 " pdb=" O CYS A 901 " model vdw 2.218 2.520 nonbonded pdb=" O THR A1180 " pdb=" OG SER A1183 " model vdw 2.232 2.440 nonbonded pdb=" O LYS A 264 " pdb=" N THR A 267 " model vdw 2.273 2.520 ... (remaining 77420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.540 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.210 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 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 : 0.002 0.038 10355 Z= 0.139 Angle : 0.519 8.654 13872 Z= 0.291 Chirality : 0.036 0.152 1441 Planarity : 0.004 0.089 1753 Dihedral : 15.626 89.391 3913 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.09 % Allowed : 0.80 % Favored : 99.11 % 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: 0.85 (0.25), residues: 1135 helix: 2.01 (0.19), residues: 701 sheet: 0.85 (1.48), residues: 10 loop : -2.09 (0.28), residues: 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 1.332 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.2430 time to fit residues: 51.7392 Evaluate side-chains 118 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0956 time to fit residues: 1.8875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 ASN ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10355 Z= 0.200 Angle : 0.497 8.157 13872 Z= 0.265 Chirality : 0.037 0.151 1441 Planarity : 0.003 0.050 1753 Dihedral : 3.481 18.107 1295 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.53 % Allowed : 8.73 % Favored : 90.73 % 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: 1.04 (0.26), residues: 1135 helix: 2.15 (0.19), residues: 706 sheet: 0.66 (1.50), residues: 10 loop : -2.03 (0.29), residues: 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.114 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 0.2251 time to fit residues: 39.8837 Evaluate side-chains 115 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0902 time to fit residues: 2.4189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 ASN A1340 HIS A1343 GLN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1962 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10355 Z= 0.256 Angle : 0.504 7.754 13872 Z= 0.269 Chirality : 0.038 0.160 1441 Planarity : 0.003 0.039 1753 Dihedral : 3.598 17.278 1295 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.98 % Allowed : 12.83 % Favored : 86.19 % 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: 0.92 (0.26), residues: 1135 helix: 2.03 (0.20), residues: 713 sheet: 0.43 (1.49), residues: 10 loop : -2.09 (0.29), residues: 412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.290 Fit side-chains outliers start: 11 outliers final: 1 residues processed: 131 average time/residue: 0.2361 time to fit residues: 43.8514 Evaluate side-chains 115 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0915 time to fit residues: 1.7637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 ASN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10355 Z= 0.177 Angle : 0.478 12.122 13872 Z= 0.251 Chirality : 0.036 0.162 1441 Planarity : 0.003 0.043 1753 Dihedral : 3.477 16.032 1295 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.34 % Allowed : 14.80 % Favored : 83.87 % 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: 1.05 (0.26), residues: 1135 helix: 2.14 (0.20), residues: 713 sheet: 0.40 (1.51), residues: 10 loop : -2.06 (0.30), residues: 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.201 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 123 average time/residue: 0.2380 time to fit residues: 42.1437 Evaluate side-chains 117 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0972 time to fit residues: 2.7371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 ASN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10355 Z= 0.336 Angle : 0.553 8.488 13872 Z= 0.292 Chirality : 0.039 0.165 1441 Planarity : 0.004 0.042 1753 Dihedral : 3.793 15.605 1295 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.60 % Allowed : 16.67 % Favored : 81.73 % 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: 0.67 (0.26), residues: 1135 helix: 1.80 (0.20), residues: 728 sheet: -0.08 (1.41), residues: 10 loop : -2.26 (0.30), residues: 397 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.271 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 0.2302 time to fit residues: 44.9015 Evaluate side-chains 121 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0946 time to fit residues: 3.6932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10355 Z= 0.170 Angle : 0.485 6.682 13872 Z= 0.256 Chirality : 0.036 0.134 1441 Planarity : 0.003 0.043 1753 Dihedral : 3.530 16.626 1295 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.16 % Allowed : 17.74 % Favored : 81.11 % 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: 0.98 (0.26), residues: 1135 helix: 2.05 (0.20), residues: 720 sheet: 0.33 (1.48), residues: 10 loop : -2.08 (0.30), residues: 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.171 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 127 average time/residue: 0.2464 time to fit residues: 44.3793 Evaluate side-chains 116 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1018 time to fit residues: 2.6853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 72 optimal weight: 0.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 GLN A1099 ASN A1781 GLN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10355 Z= 0.148 Angle : 0.481 6.989 13872 Z= 0.253 Chirality : 0.035 0.136 1441 Planarity : 0.003 0.044 1753 Dihedral : 3.391 17.291 1295 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.98 % Allowed : 18.18 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1135 helix: 2.17 (0.20), residues: 720 sheet: 0.48 (1.46), residues: 10 loop : -2.11 (0.30), residues: 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.272 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 123 average time/residue: 0.2594 time to fit residues: 45.6236 Evaluate side-chains 113 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0957 time to fit residues: 2.1927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A1099 ASN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10355 Z= 0.213 Angle : 0.501 7.832 13872 Z= 0.263 Chirality : 0.037 0.139 1441 Planarity : 0.003 0.050 1753 Dihedral : 3.456 16.899 1295 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.07 % Allowed : 18.27 % Favored : 80.66 % 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: 1.01 (0.26), residues: 1135 helix: 2.09 (0.20), residues: 723 sheet: 0.30 (1.47), residues: 10 loop : -2.13 (0.30), residues: 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.461 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 0.2413 time to fit residues: 40.7525 Evaluate side-chains 116 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1006 time to fit residues: 2.9532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 109 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 86 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10355 Z= 0.160 Angle : 0.506 10.409 13872 Z= 0.265 Chirality : 0.036 0.135 1441 Planarity : 0.003 0.048 1753 Dihedral : 3.390 16.002 1295 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.36 % Allowed : 18.45 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1135 helix: 2.22 (0.19), residues: 715 sheet: 0.48 (1.48), residues: 10 loop : -2.16 (0.29), residues: 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.239 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 118 average time/residue: 0.2350 time to fit residues: 40.2834 Evaluate side-chains 109 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0954 time to fit residues: 2.1092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10355 Z= 0.242 Angle : 0.537 8.164 13872 Z= 0.284 Chirality : 0.037 0.140 1441 Planarity : 0.003 0.045 1753 Dihedral : 3.507 15.886 1295 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.18 % Allowed : 19.07 % Favored : 80.75 % 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: 0.90 (0.26), residues: 1135 helix: 2.01 (0.20), residues: 729 sheet: 0.19 (1.45), residues: 10 loop : -2.27 (0.30), residues: 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 1.294 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 114 average time/residue: 0.2424 time to fit residues: 39.3527 Evaluate side-chains 116 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1080 time to fit residues: 2.0044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.0000 chunk 89 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.134809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.109978 restraints weight = 19982.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.110775 restraints weight = 13839.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111994 restraints weight = 13302.755| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10355 Z= 0.171 Angle : 0.518 10.604 13872 Z= 0.270 Chirality : 0.036 0.136 1441 Planarity : 0.003 0.043 1753 Dihedral : 3.417 15.289 1295 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.18 % Allowed : 18.89 % Favored : 80.93 % 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: 1.07 (0.26), residues: 1135 helix: 2.21 (0.19), residues: 717 sheet: 0.41 (1.47), residues: 10 loop : -2.21 (0.29), residues: 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.28 seconds wall clock time: 35 minutes 53.46 seconds (2153.46 seconds total)