Starting phenix.real_space_refine on Mon Jul 28 11:07:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fas_31505/07_2025/7fas_31505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fas_31505/07_2025/7fas_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/cci-nas-00/data/ceres_data/7fas_31505/07_2025/7fas_31505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fas_31505/07_2025/7fas_31505.map" model { file = "/net/cci-nas-00/data/ceres_data/7fas_31505/07_2025/7fas_31505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fas_31505/07_2025/7fas_31505.cif" } 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. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.00, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 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: 1.22 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: 3.73 Time building geometry restraints manager: 3.17 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: 0.00 - 1.73: 13664 1.73 - 3.46: 167 3.46 - 5.19: 27 5.19 - 6.92: 12 6.92 - 8.65: 2 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 3.120 nonbonded pdb=" O ASP A 169 " pdb=" NE2 GLN A 274 " model vdw 2.207 3.120 nonbonded pdb=" NH1 ARG A 772 " pdb=" O CYS A 901 " model vdw 2.218 3.120 nonbonded pdb=" O THR A1180 " pdb=" OG SER A1183 " model vdw 2.232 3.040 nonbonded pdb=" O LYS A 264 " pdb=" N THR A 267 " model vdw 2.273 3.120 ... (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: 181.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.550 ------------------------------------------------------------------------------- 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 : 0.004 0.356 10369 Z= 0.208 Angle : 0.536 14.643 13900 Z= 0.297 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 335 HIS 0.005 0.001 HIS A 260 PHE 0.012 0.001 PHE A1164 TYR 0.017 0.001 TYR A 261 ARG 0.004 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.11998 ( 541) hydrogen bonds : angle 4.52573 ( 1611) SS BOND : bond 0.09512 ( 14) SS BOND : angle 2.99826 ( 28) covalent geometry : bond 0.00225 (10355) covalent geometry : angle 0.51887 (13872) *********************** 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 to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7707 (t0) cc_final: 0.7381 (t0) REVERT: A 1812 MET cc_start: 0.8979 (ttm) cc_final: 0.8742 (ttm) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 0.2573 time to fit residues: 55.1789 Evaluate side-chains 120 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1956 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 601 GLN A 832 GLN ** A 974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.138365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110952 restraints weight = 20192.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113169 restraints weight = 10264.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112867 restraints weight = 7926.375| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10369 Z= 0.145 Angle : 0.515 8.183 13900 Z= 0.276 Chirality : 0.038 0.150 1441 Planarity : 0.004 0.051 1753 Dihedral : 3.554 20.852 1296 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.27 % Allowed : 9.00 % 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: 0.94 (0.26), residues: 1135 helix: 2.07 (0.19), residues: 712 sheet: 0.60 (1.51), residues: 10 loop : -2.12 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 282 HIS 0.004 0.001 HIS A1951 PHE 0.033 0.002 PHE A1164 TYR 0.020 0.001 TYR A1512 ARG 0.004 0.000 ARG A1610 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 541) hydrogen bonds : angle 3.75491 ( 1611) SS BOND : bond 0.00315 ( 14) SS BOND : angle 1.12383 ( 28) covalent geometry : bond 0.00334 (10355) covalent geometry : angle 0.51352 (13872) *********************** 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 129 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 1.233 Fit side-chains REVERT: A 160 ASP cc_start: 0.7805 (t0) cc_final: 0.7399 (t0) REVERT: A 335 TRP cc_start: 0.5347 (t60) cc_final: 0.4694 (t60) REVERT: A 1035 TYR cc_start: 0.7418 (t80) cc_final: 0.7000 (t80) REVERT: A 1143 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 1812 MET cc_start: 0.9037 (ttm) cc_final: 0.8818 (ttm) outliers start: 3 outliers final: 2 residues processed: 129 average time/residue: 0.2519 time to fit residues: 46.4640 Evaluate side-chains 119 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1673 ILE Chi-restraints excluded: chain A residue 1683 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 108 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 974 ASN A1036 GLN A1099 ASN ** A1343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1962 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.135869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106098 restraints weight = 20331.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109331 restraints weight = 10769.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111369 restraints weight = 7261.426| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10369 Z= 0.187 Angle : 0.531 7.841 13900 Z= 0.284 Chirality : 0.039 0.163 1441 Planarity : 0.004 0.041 1753 Dihedral : 3.676 17.859 1295 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.25 % Allowed : 12.30 % Favored : 86.45 % 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: 0.84 (0.26), residues: 1135 helix: 1.96 (0.19), residues: 711 sheet: 0.10 (1.47), residues: 10 loop : -2.10 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 282 HIS 0.005 0.001 HIS A 723 PHE 0.026 0.002 PHE A1164 TYR 0.016 0.001 TYR A1512 ARG 0.004 0.001 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 541) hydrogen bonds : angle 3.71956 ( 1611) SS BOND : bond 0.00407 ( 14) SS BOND : angle 1.29332 ( 28) covalent geometry : bond 0.00436 (10355) covalent geometry : angle 0.52818 (13872) *********************** 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 140 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7812 (t0) cc_final: 0.7375 (t0) REVERT: A 269 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7385 (pp) REVERT: A 1143 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7368 (mt-10) REVERT: A 1812 MET cc_start: 0.9094 (ttm) cc_final: 0.8665 (ttm) REVERT: A 1834 LYS cc_start: 0.8291 (tmmt) cc_final: 0.7553 (tmmt) REVERT: A 1848 ARG cc_start: 0.4030 (mmt180) cc_final: 0.3813 (mmt180) outliers start: 14 outliers final: 5 residues processed: 135 average time/residue: 0.2314 time to fit residues: 44.2405 Evaluate side-chains 117 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1673 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1956 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 ASN ** A1951 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.136752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108296 restraints weight = 20220.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.110041 restraints weight = 11100.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.111381 restraints weight = 7849.120| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10369 Z= 0.147 Angle : 0.503 8.200 13900 Z= 0.268 Chirality : 0.037 0.166 1441 Planarity : 0.003 0.042 1753 Dihedral : 3.583 16.236 1295 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.43 % Allowed : 14.71 % 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: 0.93 (0.26), residues: 1135 helix: 2.03 (0.19), residues: 716 sheet: 0.45 (1.41), residues: 10 loop : -2.11 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 282 HIS 0.003 0.001 HIS A1962 PHE 0.014 0.002 PHE A 650 TYR 0.015 0.001 TYR A1512 ARG 0.003 0.000 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 541) hydrogen bonds : angle 3.61598 ( 1611) SS BOND : bond 0.00354 ( 14) SS BOND : angle 1.44905 ( 28) covalent geometry : bond 0.00342 (10355) covalent geometry : angle 0.49921 (13872) *********************** 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 129 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7744 (t0) cc_final: 0.7348 (t0) REVERT: A 653 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7989 (m-10) REVERT: A 1812 MET cc_start: 0.9040 (ttm) cc_final: 0.8618 (ttm) REVERT: A 1834 LYS cc_start: 0.8216 (tmmt) cc_final: 0.7596 (tttt) REVERT: A 1848 ARG cc_start: 0.4210 (mmt180) cc_final: 0.3120 (mmt90) outliers start: 16 outliers final: 7 residues processed: 123 average time/residue: 0.2838 time to fit residues: 50.4222 Evaluate side-chains 116 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1673 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1956 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1099 ASN A1579 HIS ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.137756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.111706 restraints weight = 19974.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114054 restraints weight = 12378.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114579 restraints weight = 10346.257| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10369 Z= 0.144 Angle : 0.498 8.069 13900 Z= 0.264 Chirality : 0.037 0.156 1441 Planarity : 0.003 0.042 1753 Dihedral : 3.544 16.102 1295 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 16.04 % Favored : 81.91 % 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: 0.91 (0.26), residues: 1135 helix: 1.99 (0.19), residues: 726 sheet: 0.14 (1.42), residues: 10 loop : -2.14 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 282 HIS 0.004 0.001 HIS A1579 PHE 0.020 0.002 PHE A1023 TYR 0.014 0.001 TYR A1512 ARG 0.003 0.000 ARG A 256 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 541) hydrogen bonds : angle 3.55625 ( 1611) SS BOND : bond 0.00262 ( 14) SS BOND : angle 1.46738 ( 28) covalent geometry : bond 0.00335 (10355) covalent geometry : angle 0.49456 (13872) *********************** 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 144 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.6853 (mmp80) cc_final: 0.6603 (mmp80) REVERT: A 160 ASP cc_start: 0.7708 (t0) cc_final: 0.7375 (t0) REVERT: A 601 GLN cc_start: 0.4227 (OUTLIER) cc_final: 0.2900 (pm20) REVERT: A 653 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: A 1812 MET cc_start: 0.8977 (ttm) cc_final: 0.8563 (ttm) REVERT: A 1848 ARG cc_start: 0.4335 (mmt180) cc_final: 0.3214 (mmt90) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 0.2401 time to fit residues: 46.5177 Evaluate side-chains 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1673 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1955 CYS Chi-restraints excluded: chain A residue 1956 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 5.9990 chunk 92 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.138580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.111490 restraints weight = 20017.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113053 restraints weight = 11061.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.113356 restraints weight = 8153.524| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10369 Z= 0.131 Angle : 0.501 7.953 13900 Z= 0.265 Chirality : 0.037 0.137 1441 Planarity : 0.003 0.043 1753 Dihedral : 3.482 16.407 1295 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.41 % Allowed : 16.49 % 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: 0.95 (0.26), residues: 1135 helix: 2.01 (0.19), residues: 726 sheet: 0.25 (1.45), residues: 10 loop : -2.13 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 282 HIS 0.003 0.001 HIS A1962 PHE 0.018 0.002 PHE A1023 TYR 0.015 0.001 TYR A1886 ARG 0.004 0.000 ARG A1610 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 541) hydrogen bonds : angle 3.51695 ( 1611) SS BOND : bond 0.00201 ( 14) SS BOND : angle 1.39145 ( 28) covalent geometry : bond 0.00301 (10355) covalent geometry : angle 0.49792 (13872) *********************** 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 147 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 160 ASP cc_start: 0.7724 (t0) cc_final: 0.7355 (t0) REVERT: A 284 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 601 GLN cc_start: 0.4168 (OUTLIER) cc_final: 0.2780 (pm20) REVERT: A 653 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8075 (m-10) REVERT: A 1812 MET cc_start: 0.8998 (ttm) cc_final: 0.8582 (ttm) REVERT: A 1848 ARG cc_start: 0.4269 (mmt180) cc_final: 0.3159 (mmt90) outliers start: 27 outliers final: 15 residues processed: 140 average time/residue: 0.2400 time to fit residues: 47.7108 Evaluate side-chains 127 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1673 ILE Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1895 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 108 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.139470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113061 restraints weight = 20216.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115380 restraints weight = 12153.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.116400 restraints weight = 9402.994| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10369 Z= 0.118 Angle : 0.495 7.103 13900 Z= 0.263 Chirality : 0.036 0.137 1441 Planarity : 0.003 0.047 1753 Dihedral : 3.412 13.484 1295 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.23 % Allowed : 17.29 % Favored : 80.48 % 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: 2.11 (0.19), residues: 716 sheet: 0.27 (1.46), residues: 10 loop : -2.02 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1451 HIS 0.003 0.001 HIS A1962 PHE 0.015 0.001 PHE A1138 TYR 0.014 0.001 TYR A1886 ARG 0.002 0.000 ARG A1674 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 541) hydrogen bonds : angle 3.45686 ( 1611) SS BOND : bond 0.00249 ( 14) SS BOND : angle 1.37005 ( 28) covalent geometry : bond 0.00269 (10355) covalent geometry : angle 0.49133 (13872) *********************** 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 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6651 (mmp80) REVERT: A 160 ASP cc_start: 0.7717 (t0) cc_final: 0.7357 (t0) REVERT: A 284 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8224 (tm-30) REVERT: A 601 GLN cc_start: 0.4138 (OUTLIER) cc_final: 0.2828 (pm20) REVERT: A 653 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: A 1679 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: A 1812 MET cc_start: 0.8991 (ttm) cc_final: 0.8643 (ttm) REVERT: A 1848 ARG cc_start: 0.4131 (mmt180) cc_final: 0.3063 (mmt90) outliers start: 25 outliers final: 15 residues processed: 137 average time/residue: 0.2452 time to fit residues: 48.0227 Evaluate side-chains 129 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1679 ASP Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1895 ILE Chi-restraints excluded: chain A residue 1967 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS A1099 ASN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.137668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113102 restraints weight = 20171.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112998 restraints weight = 15719.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114037 restraints weight = 17818.081| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10369 Z= 0.264 Angle : 0.613 8.182 13900 Z= 0.326 Chirality : 0.041 0.151 1441 Planarity : 0.004 0.046 1753 Dihedral : 3.910 15.146 1295 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.32 % Allowed : 17.83 % Favored : 79.86 % 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: 0.50 (0.26), residues: 1135 helix: 1.68 (0.19), residues: 727 sheet: -0.21 (1.22), residues: 10 loop : -2.34 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 278 HIS 0.005 0.001 HIS A 300 PHE 0.021 0.002 PHE A1138 TYR 0.020 0.002 TYR A1886 ARG 0.005 0.001 ARG A1674 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 541) hydrogen bonds : angle 3.77409 ( 1611) SS BOND : bond 0.00388 ( 14) SS BOND : angle 1.54806 ( 28) covalent geometry : bond 0.00622 (10355) covalent geometry : angle 0.60929 (13872) *********************** 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 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.256 Fit side-chains REVERT: A 100 ARG cc_start: 0.7235 (mmm160) cc_final: 0.6795 (mmp80) REVERT: A 160 ASP cc_start: 0.7645 (t0) cc_final: 0.7281 (t0) REVERT: A 284 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 653 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: A 867 LYS cc_start: 0.6304 (pttt) cc_final: 0.5932 (mmtt) REVERT: A 942 SER cc_start: 0.8925 (p) cc_final: 0.8633 (m) REVERT: A 1679 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: A 1812 MET cc_start: 0.8825 (ttm) cc_final: 0.8526 (ttm) REVERT: A 1848 ARG cc_start: 0.4507 (mmt180) cc_final: 0.3896 (mmt-90) REVERT: A 1967 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8472 (mm) outliers start: 26 outliers final: 19 residues processed: 135 average time/residue: 0.2276 time to fit residues: 44.1525 Evaluate side-chains 133 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1673 ILE Chi-restraints excluded: chain A residue 1679 ASP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1955 CYS Chi-restraints excluded: chain A residue 1956 THR Chi-restraints excluded: chain A residue 1967 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 0.5980 chunk 108 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 665 ASN A1099 ASN ** A1951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.140990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116293 restraints weight = 20000.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116549 restraints weight = 14584.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117692 restraints weight = 15127.461| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10369 Z= 0.126 Angle : 0.533 10.668 13900 Z= 0.281 Chirality : 0.037 0.137 1441 Planarity : 0.003 0.043 1753 Dihedral : 3.627 14.634 1295 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.32 % Allowed : 18.18 % Favored : 79.50 % 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: 0.79 (0.26), residues: 1135 helix: 1.88 (0.19), residues: 726 sheet: 0.47 (1.38), residues: 10 loop : -2.17 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1451 HIS 0.003 0.001 HIS A1962 PHE 0.021 0.002 PHE A1138 TYR 0.015 0.001 TYR A1862 ARG 0.002 0.000 ARG A1863 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 541) hydrogen bonds : angle 3.54358 ( 1611) SS BOND : bond 0.00245 ( 14) SS BOND : angle 1.30398 ( 28) covalent geometry : bond 0.00287 (10355) covalent geometry : angle 0.53045 (13872) *********************** 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 144 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7204 (mmm160) cc_final: 0.6777 (mmp80) REVERT: A 160 ASP cc_start: 0.7559 (t0) cc_final: 0.7273 (t0) REVERT: A 284 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 574 TYR cc_start: 0.8524 (m-80) cc_final: 0.8277 (m-80) REVERT: A 601 GLN cc_start: 0.4327 (OUTLIER) cc_final: 0.3017 (pm20) REVERT: A 653 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: A 867 LYS cc_start: 0.6293 (pttt) cc_final: 0.5899 (mmtt) REVERT: A 942 SER cc_start: 0.9025 (p) cc_final: 0.8682 (m) REVERT: A 1137 PHE cc_start: 0.7316 (t80) cc_final: 0.7112 (t80) REVERT: A 1679 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: A 1812 MET cc_start: 0.8824 (ttm) cc_final: 0.8525 (ttm) REVERT: A 1834 LYS cc_start: 0.8312 (tmmt) cc_final: 0.7687 (tttt) REVERT: A 1848 ARG cc_start: 0.4466 (mmt180) cc_final: 0.3166 (mmt90) outliers start: 26 outliers final: 21 residues processed: 135 average time/residue: 0.2331 time to fit residues: 44.6443 Evaluate side-chains 137 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 665 ASN Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1679 ASP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1955 CYS Chi-restraints excluded: chain A residue 1956 THR Chi-restraints excluded: chain A residue 1960 LEU Chi-restraints excluded: chain A residue 1967 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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** A1099 ASN ** A1951 HIS ** 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 = 0.4053 r_free = 0.4053 target = 0.138098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.110746 restraints weight = 20099.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112525 restraints weight = 11152.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.113606 restraints weight = 8119.029| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10369 Z= 0.140 Angle : 0.534 7.551 13900 Z= 0.284 Chirality : 0.037 0.145 1441 Planarity : 0.003 0.044 1753 Dihedral : 3.590 14.751 1295 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.50 % Allowed : 18.27 % Favored : 79.23 % 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: 0.81 (0.26), residues: 1135 helix: 1.89 (0.19), residues: 726 sheet: 0.47 (1.39), residues: 10 loop : -2.15 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1451 HIS 0.003 0.001 HIS A1962 PHE 0.020 0.002 PHE A1138 TYR 0.033 0.001 TYR A1862 ARG 0.003 0.000 ARG A1674 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 541) hydrogen bonds : angle 3.52637 ( 1611) SS BOND : bond 0.00250 ( 14) SS BOND : angle 1.30004 ( 28) covalent geometry : bond 0.00324 (10355) covalent geometry : angle 0.53160 (13872) ********************** 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 143 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7400 (mmm160) cc_final: 0.6676 (mmp80) REVERT: A 160 ASP cc_start: 0.7695 (t0) cc_final: 0.7315 (t0) REVERT: A 284 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 574 TYR cc_start: 0.8571 (m-80) cc_final: 0.8313 (m-80) REVERT: A 601 GLN cc_start: 0.4241 (OUTLIER) cc_final: 0.2859 (pm20) REVERT: A 653 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: A 867 LYS cc_start: 0.6144 (pttt) cc_final: 0.5678 (mmtt) REVERT: A 942 SER cc_start: 0.9003 (p) cc_final: 0.8718 (m) REVERT: A 1137 PHE cc_start: 0.7266 (t80) cc_final: 0.7063 (t80) REVERT: A 1679 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: A 1812 MET cc_start: 0.8979 (ttm) cc_final: 0.8654 (ttm) REVERT: A 1834 LYS cc_start: 0.8206 (tmmt) cc_final: 0.7554 (tttt) REVERT: A 1848 ARG cc_start: 0.4240 (mmt180) cc_final: 0.3008 (mmt90) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 0.2348 time to fit residues: 45.0753 Evaluate side-chains 138 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 592 CYS Chi-restraints excluded: chain A residue 601 GLN Chi-restraints excluded: chain A residue 653 TYR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1679 ASP Chi-restraints excluded: chain A residue 1680 LEU Chi-restraints excluded: chain A residue 1683 ILE Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1956 THR Chi-restraints excluded: chain A residue 1967 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 51 optimal weight: 0.2980 chunk 4 optimal weight: 0.0010 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A1951 HIS ** 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 = 0.4076 r_free = 0.4076 target = 0.142150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117676 restraints weight = 19872.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116777 restraints weight = 17108.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117860 restraints weight = 16263.735| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10369 Z= 0.116 Angle : 0.519 10.984 13900 Z= 0.273 Chirality : 0.036 0.143 1441 Planarity : 0.003 0.043 1753 Dihedral : 3.414 13.953 1295 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.96 % Allowed : 18.81 % Favored : 79.23 % 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: 1.06 (0.26), residues: 1135 helix: 2.12 (0.19), residues: 715 sheet: 0.56 (1.43), residues: 10 loop : -2.03 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1451 HIS 0.003 0.001 HIS A 260 PHE 0.020 0.001 PHE A1138 TYR 0.021 0.001 TYR A1862 ARG 0.002 0.000 ARG A1674 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 541) hydrogen bonds : angle 3.40922 ( 1611) SS BOND : bond 0.00219 ( 14) SS BOND : angle 1.25781 ( 28) covalent geometry : bond 0.00263 (10355) covalent geometry : angle 0.51617 (13872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.19 seconds wall clock time: 61 minutes 13.92 seconds (3673.92 seconds total)