Starting phenix.real_space_refine on Sat Oct 12 16:29:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdo_43152/10_2024/8vdo_43152.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdo_43152/10_2024/8vdo_43152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdo_43152/10_2024/8vdo_43152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdo_43152/10_2024/8vdo_43152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdo_43152/10_2024/8vdo_43152.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdo_43152/10_2024/8vdo_43152.cif" } resolution = 2.7 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= -0.000 sd= 0.040 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 62 5.16 5 C 7794 2.51 5 N 2267 2.21 5 O 2568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 12691 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1740, 12658 Classifications: {'peptide': 1740} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 1674} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Conformer: "B" Number of residues, atoms: 1740, 12658 Classifications: {'peptide': 1740} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 1674} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 12754 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 589 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 589 " occ=0.50 residue: pdb=" N AARG A 891 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 891 " occ=0.50 residue: pdb=" N AARG A1136 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1136 " occ=0.50 Time building chain proxies: 13.23, per 1000 atoms: 1.04 Number of scatterers: 12691 At special positions: 0 Unit cell: (111.744, 119.808, 148.608, 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 62 16.00 O 2568 8.00 N 2267 7.00 C 7794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.41 Conformation dependent library (CDL) restraints added in 3.3 seconds 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3266 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 2 sheets defined 84.9% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 384 through 400 Processing helix chain 'A' and resid 489 through 515 removed outlier: 3.835A pdb=" N ASP A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 561 Processing helix chain 'A' and resid 569 through 600 Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 605 through 626 Processing helix chain 'A' and resid 633 through 655 removed outlier: 3.928A pdb=" N LEU A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 693 Processing helix chain 'A' and resid 695 through 724 Processing helix chain 'A' and resid 729 through 756 Processing helix chain 'A' and resid 759 through 789 removed outlier: 3.747A pdb=" N ALA A 789 " --> pdb=" O VAL A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 815 Processing helix chain 'A' and resid 818 through 847 Processing helix chain 'A' and resid 849 through 880 Processing helix chain 'A' and resid 883 through 905 removed outlier: 3.576A pdb=" N GLN A 887 " --> pdb=" O SER A 883 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 941 Processing helix chain 'A' and resid 948 through 976 Proline residue: A 964 - end of helix Processing helix chain 'A' and resid 979 through 1008 removed outlier: 4.451A pdb=" N GLN A 995 " --> pdb=" O GLN A 991 " (cutoff:3.500A) Proline residue: A 996 - end of helix Processing helix chain 'A' and resid 1009 through 1011 No H-bonds generated for 'chain 'A' and resid 1009 through 1011' Processing helix chain 'A' and resid 1013 through 1046 Processing helix chain 'A' and resid 1048 through 1073 removed outlier: 3.771A pdb=" N LEU A1054 " --> pdb=" O MET A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1112 Processing helix chain 'A' and resid 1113 through 1142 Processing helix chain 'A' and resid 1144 through 1175 removed outlier: 3.553A pdb=" N GLN A1148 " --> pdb=" O ASP A1144 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A1175 " --> pdb=" O LYS A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1202 Processing helix chain 'A' and resid 1203 through 1205 No H-bonds generated for 'chain 'A' and resid 1203 through 1205' Processing helix chain 'A' and resid 1206 through 1225 Processing helix chain 'A' and resid 1234 through 1260 Processing helix chain 'A' and resid 1263 through 1291 Processing helix chain 'A' and resid 1294 through 1325 removed outlier: 3.889A pdb=" N THR A1324 " --> pdb=" O LYS A1320 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A1325 " --> pdb=" O ALA A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1353 Processing helix chain 'A' and resid 1359 through 1374 removed outlier: 3.582A pdb=" N CYS A1363 " --> pdb=" O GLY A1359 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A1372 " --> pdb=" O ARG A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1378 removed outlier: 3.629A pdb=" N GLU A1378 " --> pdb=" O GLU A1375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1375 through 1378' Processing helix chain 'A' and resid 1388 through 1417 Processing helix chain 'A' and resid 1418 through 1450 Processing helix chain 'A' and resid 1463 through 1483 Processing helix chain 'A' and resid 1487 through 1516 Processing helix chain 'A' and resid 1518 through 1547 Processing helix chain 'A' and resid 1551 through 1577 removed outlier: 3.884A pdb=" N ALA A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix Processing helix chain 'A' and resid 1589 through 1623 Proline residue: A1598 - end of helix Processing helix chain 'A' and resid 1626 through 1655 removed outlier: 3.720A pdb=" N SER A1631 " --> pdb=" O PRO A1627 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A1655 " --> pdb=" O MET A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1684 Processing helix chain 'A' and resid 1694 through 1722 removed outlier: 3.555A pdb=" N LEU A1698 " --> pdb=" O SER A1694 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A1714 " --> pdb=" O SER A1710 " (cutoff:3.500A) Proline residue: A1715 - end of helix Processing helix chain 'A' and resid 1723 through 1736 removed outlier: 3.507A pdb=" N LEU A1727 " --> pdb=" O GLU A1723 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A1728 " --> pdb=" O ALA A1724 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS A1729 " --> pdb=" O SER A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1754 through 1783 Processing helix chain 'A' and resid 1789 through 1821 removed outlier: 3.721A pdb=" N ALA A1821 " --> pdb=" O ALA A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1838 Processing helix chain 'A' and resid 1849 through 1878 removed outlier: 3.924A pdb=" N ASN A1876 " --> pdb=" O VAL A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1881 through 1907 removed outlier: 3.985A pdb=" N LYS A1901 " --> pdb=" O ALA A1897 " (cutoff:3.500A) Proline residue: A1902 - end of helix Processing helix chain 'A' and resid 1909 through 1940 Processing helix chain 'A' and resid 1943 through 1972 removed outlier: 3.520A pdb=" N LYS A1947 " --> pdb=" O ASP A1943 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY A1971 " --> pdb=" O ALA A1967 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A1972 " --> pdb=" O LEU A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 2001 removed outlier: 4.143A pdb=" N ALA A2001 " --> pdb=" O MET A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2014 through 2037 removed outlier: 4.268A pdb=" N GLY A2018 " --> pdb=" O ASP A2014 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2070 removed outlier: 3.562A pdb=" N GLY A2070 " --> pdb=" O ALA A2066 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2102 removed outlier: 3.547A pdb=" N GLN A2077 " --> pdb=" O ASP A2073 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A2080 " --> pdb=" O THR A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2135 removed outlier: 4.123A pdb=" N TRP A2112 " --> pdb=" O ASP A2108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.670A pdb=" N SER A 311 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A 337 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU A 350 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 339 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361 1226 hydrogen bonds defined for protein. 3672 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: 4.97 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2651 1.33 - 1.45: 2458 1.45 - 1.57: 7620 1.57 - 1.69: 0 1.69 - 1.81: 97 Bond restraints: 12826 Sorted by residual: bond pdb=" C GLU A1463 " pdb=" N PRO A1464 " ideal model delta sigma weight residual 1.336 1.371 -0.035 1.20e-02 6.94e+03 8.75e+00 bond pdb=" C PRO A1464 " pdb=" O PRO A1464 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.20e-02 6.94e+03 6.68e+00 bond pdb=" N THR A1465 " pdb=" CA THR A1465 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.57e+00 bond pdb=" N ARG A1469 " pdb=" CA ARG A1469 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 bond pdb=" N GLN A1466 " pdb=" CA GLN A1466 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.22e+00 ... (remaining 12821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16968 2.02 - 4.04: 373 4.04 - 6.06: 49 6.06 - 8.08: 8 8.08 - 10.09: 2 Bond angle restraints: 17400 Sorted by residual: angle pdb=" C THR A 772 " pdb=" CA THR A 772 " pdb=" CB THR A 772 " ideal model delta sigma weight residual 110.79 117.82 -7.03 1.66e+00 3.63e-01 1.79e+01 angle pdb=" CA LEU A1020 " pdb=" C LEU A1020 " pdb=" O LEU A1020 " ideal model delta sigma weight residual 120.55 116.77 3.78 1.06e+00 8.90e-01 1.27e+01 angle pdb=" C GLN A 783 " pdb=" N HIS A 784 " pdb=" CA HIS A 784 " ideal model delta sigma weight residual 122.06 115.49 6.57 1.86e+00 2.89e-01 1.25e+01 angle pdb=" CA SER A1021 " pdb=" C SER A1021 " pdb=" O SER A1021 " ideal model delta sigma weight residual 120.55 116.89 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CB MET A1759 " pdb=" CG MET A1759 " pdb=" SD MET A1759 " ideal model delta sigma weight residual 112.70 102.61 10.09 3.00e+00 1.11e-01 1.13e+01 ... (remaining 17395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7287 17.96 - 35.92: 532 35.92 - 53.88: 102 53.88 - 71.85: 59 71.85 - 89.81: 21 Dihedral angle restraints: 8001 sinusoidal: 2977 harmonic: 5024 Sorted by residual: dihedral pdb=" CA GLU A 599 " pdb=" C GLU A 599 " pdb=" N ASP A 600 " pdb=" CA ASP A 600 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA VAL A 380 " pdb=" C VAL A 380 " pdb=" N GLN A 381 " pdb=" CA GLN A 381 " ideal model delta harmonic sigma weight residual 180.00 -161.09 -18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" C THR A 772 " pdb=" N THR A 772 " pdb=" CA THR A 772 " pdb=" CB THR A 772 " ideal model delta harmonic sigma weight residual -122.00 -131.32 9.32 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 7998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1591 0.043 - 0.086: 406 0.086 - 0.129: 84 0.129 - 0.172: 15 0.172 - 0.215: 6 Chirality restraints: 2102 Sorted by residual: chirality pdb=" CG LEU A 609 " pdb=" CB LEU A 609 " pdb=" CD1 LEU A 609 " pdb=" CD2 LEU A 609 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL A 380 " pdb=" CA VAL A 380 " pdb=" CG1 VAL A 380 " pdb=" CG2 VAL A 380 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG A1035 " pdb=" N ARG A1035 " pdb=" C ARG A1035 " pdb=" CB ARG A1035 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2099 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 772 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.14e+00 pdb=" C THR A 772 " -0.046 2.00e-02 2.50e+03 pdb=" O THR A 772 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 773 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 564 " -0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 565 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A1018 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C MET A1018 " 0.037 2.00e-02 2.50e+03 pdb=" O MET A1018 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A1019 " -0.013 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1296 2.74 - 3.28: 13686 3.28 - 3.82: 23089 3.82 - 4.36: 25619 4.36 - 4.90: 44352 Nonbonded interactions: 108042 Sorted by model distance: nonbonded pdb=" ND2 ASN A1250 " pdb=" OE1 GLU A1371 " model vdw 2.198 3.120 nonbonded pdb=" OE2 GLU A1168 " pdb=" NH1 ARG A1184 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASN A1211 " pdb=" NH2 ARG A1214 " model vdw 2.203 3.120 nonbonded pdb=" O VAL A1640 " pdb=" OG SER A1643 " model vdw 2.205 3.040 nonbonded pdb=" O LYS A2031 " pdb=" NE2 GLN A2035 " model vdw 2.231 3.120 ... (remaining 108037 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 40.070 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.110 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.005 0.075 12826 Z= 0.311 Angle : 0.718 10.095 17400 Z= 0.425 Chirality : 0.041 0.215 2102 Planarity : 0.005 0.059 2313 Dihedral : 15.243 89.807 4735 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.45 % Allowed : 0.30 % Favored : 99.25 % 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: 1.94 (0.19), residues: 1745 helix: 1.81 (0.13), residues: 1428 sheet: -0.22 (0.70), residues: 53 loop : -1.23 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 351 HIS 0.004 0.001 HIS A 784 PHE 0.022 0.002 PHE A1390 TYR 0.023 0.002 TYR A1893 ARG 0.008 0.001 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.309 Fit side-chains REVERT: A 772 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6740 (t) REVERT: A 1184 ARG cc_start: 0.6547 (mtm110) cc_final: 0.5996 (mtp85) REVERT: A 1304 ASN cc_start: 0.7159 (m-40) cc_final: 0.6952 (m-40) REVERT: A 1531 GLU cc_start: 0.7420 (tp30) cc_final: 0.6990 (tp30) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 1.3736 time to fit residues: 231.3277 Evaluate side-chains 113 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 772 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 HIS A1686 GLN A1837 GLN A1854 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12826 Z= 0.272 Angle : 0.607 7.924 17400 Z= 0.321 Chirality : 0.041 0.211 2102 Planarity : 0.005 0.054 2313 Dihedral : 4.358 29.814 1824 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.96 % Allowed : 7.61 % Favored : 90.44 % 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: 2.86 (0.19), residues: 1745 helix: 2.45 (0.13), residues: 1440 sheet: 0.09 (0.72), residues: 53 loop : -1.16 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 351 HIS 0.015 0.002 HIS A 784 PHE 0.019 0.002 PHE A1390 TYR 0.022 0.002 TYR A1893 ARG 0.006 0.001 ARG A1184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 1.255 Fit side-chains REVERT: A 1184 ARG cc_start: 0.6665 (mtm110) cc_final: 0.6357 (mtp-110) REVERT: A 1397 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6521 (mtm) REVERT: A 1455 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: A 1531 GLU cc_start: 0.7419 (tp30) cc_final: 0.6988 (tp30) REVERT: A 1910 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6771 (mt-10) outliers start: 22 outliers final: 10 residues processed: 126 average time/residue: 1.3917 time to fit residues: 191.1674 Evaluate side-chains 123 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 2111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 171 optimal weight: 0.0980 chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12826 Z= 0.211 Angle : 0.546 8.789 17400 Z= 0.286 Chirality : 0.039 0.203 2102 Planarity : 0.004 0.053 2313 Dihedral : 4.048 18.459 1823 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.18 % Allowed : 8.81 % Favored : 89.01 % 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: 3.56 (0.19), residues: 1745 helix: 2.97 (0.12), residues: 1444 sheet: 0.00 (0.71), residues: 53 loop : -1.17 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 351 HIS 0.010 0.001 HIS A 784 PHE 0.015 0.002 PHE A1390 TYR 0.021 0.002 TYR A1893 ARG 0.005 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.475 Fit side-chains REVERT: A 1153 ASP cc_start: 0.6879 (m-30) cc_final: 0.6580 (m-30) REVERT: A 1184 ARG cc_start: 0.6625 (mtm110) cc_final: 0.6327 (mtp-110) REVERT: A 1397 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6606 (mtm) REVERT: A 1431 LYS cc_start: 0.8172 (tttt) cc_final: 0.6956 (tmtt) REVERT: A 1455 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7179 (mt0) REVERT: A 1531 GLU cc_start: 0.7234 (tp30) cc_final: 0.6852 (tp30) REVERT: A 1644 ILE cc_start: 0.7225 (mt) cc_final: 0.6760 (mp) REVERT: A 2031 LYS cc_start: 0.6096 (mmtt) cc_final: 0.5798 (mmtt) REVERT: A 2035 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5801 (mp10) outliers start: 25 outliers final: 11 residues processed: 136 average time/residue: 1.3912 time to fit residues: 207.3563 Evaluate side-chains 126 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 1650 SER Chi-restraints excluded: chain A residue 1905 VAL Chi-restraints excluded: chain A residue 2035 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.0870 chunk 75 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12826 Z= 0.217 Angle : 0.539 7.203 17400 Z= 0.282 Chirality : 0.038 0.192 2102 Planarity : 0.004 0.055 2313 Dihedral : 3.969 19.075 1823 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.03 % Allowed : 10.02 % Favored : 87.95 % 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: 3.76 (0.19), residues: 1745 helix: 3.11 (0.12), residues: 1443 sheet: 0.04 (0.72), residues: 53 loop : -1.10 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 351 HIS 0.011 0.001 HIS A 784 PHE 0.016 0.002 PHE A1390 TYR 0.022 0.002 TYR A1893 ARG 0.004 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 378 TYR cc_start: 0.7301 (t80) cc_final: 0.7077 (t80) REVERT: A 1184 ARG cc_start: 0.6530 (mtm110) cc_final: 0.6199 (mtp-110) REVERT: A 1346 ILE cc_start: 0.6150 (mm) cc_final: 0.5926 (mt) REVERT: A 1397 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6336 (mtm) REVERT: A 1431 LYS cc_start: 0.8176 (tttt) cc_final: 0.6934 (tmtt) REVERT: A 1455 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7278 (mt0) REVERT: A 1531 GLU cc_start: 0.7182 (tp30) cc_final: 0.6807 (tp30) REVERT: A 1644 ILE cc_start: 0.7237 (mt) cc_final: 0.6726 (mp) REVERT: A 1803 MET cc_start: 0.8158 (ttt) cc_final: 0.7823 (ttt) REVERT: A 1843 MET cc_start: 0.4027 (ttt) cc_final: 0.3820 (mtm) outliers start: 23 outliers final: 13 residues processed: 132 average time/residue: 1.3765 time to fit residues: 199.4561 Evaluate side-chains 129 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 1650 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 0.0050 chunk 0 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1304 ASN A2035 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12826 Z= 0.221 Angle : 0.537 8.677 17400 Z= 0.279 Chirality : 0.038 0.177 2102 Planarity : 0.004 0.056 2313 Dihedral : 3.935 18.836 1823 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.11 % Allowed : 10.32 % Favored : 87.58 % 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: 3.84 (0.19), residues: 1745 helix: 3.17 (0.12), residues: 1444 sheet: 0.02 (0.72), residues: 53 loop : -1.12 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 351 HIS 0.011 0.001 HIS A 784 PHE 0.016 0.001 PHE A1390 TYR 0.022 0.002 TYR A1893 ARG 0.004 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 703 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6687 (mp) REVERT: A 1346 ILE cc_start: 0.6323 (mm) cc_final: 0.5981 (mt) REVERT: A 1397 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.6347 (mtm) REVERT: A 1431 LYS cc_start: 0.8117 (tttt) cc_final: 0.6911 (tmtt) REVERT: A 1455 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7283 (mt0) REVERT: A 1531 GLU cc_start: 0.7186 (tp30) cc_final: 0.6806 (tp30) REVERT: A 1644 ILE cc_start: 0.7139 (mt) cc_final: 0.6644 (mp) REVERT: A 1803 MET cc_start: 0.8160 (ttt) cc_final: 0.7781 (ttt) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 1.3355 time to fit residues: 194.4386 Evaluate side-chains 137 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 2035 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 98 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12826 Z= 0.217 Angle : 0.531 8.311 17400 Z= 0.278 Chirality : 0.038 0.173 2102 Planarity : 0.004 0.056 2313 Dihedral : 3.907 18.863 1823 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.18 % Allowed : 10.62 % Favored : 87.20 % 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: 3.85 (0.19), residues: 1745 helix: 3.17 (0.12), residues: 1445 sheet: 0.05 (0.72), residues: 53 loop : -1.09 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 351 HIS 0.011 0.001 HIS A 784 PHE 0.015 0.001 PHE A1390 TYR 0.021 0.002 TYR A1893 ARG 0.004 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7908 (tpp) REVERT: A 703 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6660 (mp) REVERT: A 1288 MET cc_start: 0.5710 (ttp) cc_final: 0.5460 (tmm) REVERT: A 1346 ILE cc_start: 0.6312 (mm) cc_final: 0.5969 (mt) REVERT: A 1397 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6347 (mtm) REVERT: A 1431 LYS cc_start: 0.8116 (tttt) cc_final: 0.6907 (tmtt) REVERT: A 1455 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: A 1531 GLU cc_start: 0.7186 (tp30) cc_final: 0.6801 (tp30) REVERT: A 1644 ILE cc_start: 0.7144 (mt) cc_final: 0.6642 (mp) REVERT: A 1803 MET cc_start: 0.8162 (ttt) cc_final: 0.7791 (ttt) outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 1.3083 time to fit residues: 189.2290 Evaluate side-chains 134 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 1058 GLN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1573 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 GLN ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2035 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12826 Z= 0.354 Angle : 0.626 9.316 17400 Z= 0.325 Chirality : 0.044 0.227 2102 Planarity : 0.004 0.059 2313 Dihedral : 4.165 20.591 1823 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.18 % Allowed : 10.84 % Favored : 86.97 % 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: 3.20 (0.19), residues: 1745 helix: 2.70 (0.12), residues: 1444 sheet: 0.08 (0.73), residues: 53 loop : -1.19 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A2112 HIS 0.011 0.002 HIS A 784 PHE 0.021 0.002 PHE A1390 TYR 0.024 0.003 TYR A1893 ARG 0.006 0.001 ARG A 898 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.7792 (tp) cc_final: 0.7512 (mp) REVERT: A 703 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6979 (mp) REVERT: A 1397 MET cc_start: 0.6756 (OUTLIER) cc_final: 0.6554 (mtm) REVERT: A 1431 LYS cc_start: 0.8224 (tttt) cc_final: 0.7014 (tmtt) REVERT: A 1455 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7343 (mt0) REVERT: A 1469 ARG cc_start: 0.6564 (OUTLIER) cc_final: 0.6069 (mtt90) REVERT: A 1531 GLU cc_start: 0.7417 (tp30) cc_final: 0.6926 (tp30) REVERT: A 1644 ILE cc_start: 0.7199 (mt) cc_final: 0.6708 (mp) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 1.3548 time to fit residues: 190.8010 Evaluate side-chains 135 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 1058 GLN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1469 ARG Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1571 ASN Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 1905 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12826 Z= 0.216 Angle : 0.542 9.735 17400 Z= 0.283 Chirality : 0.038 0.181 2102 Planarity : 0.004 0.056 2313 Dihedral : 3.928 18.877 1823 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.11 % Allowed : 11.14 % Favored : 86.75 % 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: 3.76 (0.19), residues: 1745 helix: 3.10 (0.12), residues: 1445 sheet: 0.08 (0.72), residues: 53 loop : -1.09 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 351 HIS 0.010 0.001 HIS A 784 PHE 0.015 0.001 PHE A1390 TYR 0.021 0.002 TYR A1893 ARG 0.004 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 703 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6705 (mp) REVERT: A 1397 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6532 (mtm) REVERT: A 1431 LYS cc_start: 0.8164 (tttt) cc_final: 0.6986 (tmtt) REVERT: A 1455 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7207 (mt0) REVERT: A 1469 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.6121 (mtt90) REVERT: A 1531 GLU cc_start: 0.7191 (tp30) cc_final: 0.6787 (tp30) REVERT: A 1606 MET cc_start: 0.6061 (ttp) cc_final: 0.5700 (tmm) REVERT: A 1644 ILE cc_start: 0.7162 (mt) cc_final: 0.6726 (mp) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 1.4556 time to fit residues: 198.0618 Evaluate side-chains 135 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 1058 GLN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1469 ARG Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 1905 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12826 Z= 0.238 Angle : 0.565 9.275 17400 Z= 0.292 Chirality : 0.039 0.191 2102 Planarity : 0.004 0.058 2313 Dihedral : 3.945 19.019 1823 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.11 % Allowed : 11.22 % Favored : 86.67 % 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: 3.72 (0.19), residues: 1745 helix: 3.07 (0.12), residues: 1445 sheet: 0.05 (0.72), residues: 53 loop : -1.10 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 351 HIS 0.011 0.001 HIS A 784 PHE 0.017 0.002 PHE A1390 TYR 0.022 0.002 TYR A1893 ARG 0.004 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 703 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6727 (mp) REVERT: A 1346 ILE cc_start: 0.6339 (mm) cc_final: 0.5994 (mt) REVERT: A 1397 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6567 (mtm) REVERT: A 1431 LYS cc_start: 0.8153 (tttt) cc_final: 0.6960 (tmtt) REVERT: A 1455 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: A 1469 ARG cc_start: 0.6521 (OUTLIER) cc_final: 0.6131 (mtt90) REVERT: A 1476 MET cc_start: 0.7194 (mtp) cc_final: 0.6977 (mtp) REVERT: A 1531 GLU cc_start: 0.7226 (tp30) cc_final: 0.6829 (tp30) REVERT: A 1644 ILE cc_start: 0.7160 (mt) cc_final: 0.6698 (mp) outliers start: 24 outliers final: 19 residues processed: 126 average time/residue: 1.3520 time to fit residues: 186.3437 Evaluate side-chains 135 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 1058 GLN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1469 ARG Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1573 SER Chi-restraints excluded: chain A residue 1905 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.0370 chunk 84 optimal weight: 0.0040 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.7274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2035 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12826 Z= 0.219 Angle : 0.546 8.978 17400 Z= 0.284 Chirality : 0.038 0.190 2102 Planarity : 0.004 0.057 2313 Dihedral : 3.897 18.586 1823 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.11 % Allowed : 11.22 % Favored : 86.67 % 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: 3.81 (0.19), residues: 1745 helix: 3.14 (0.12), residues: 1447 sheet: 0.07 (0.72), residues: 53 loop : -1.12 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 351 HIS 0.011 0.001 HIS A 784 PHE 0.015 0.001 PHE A1390 TYR 0.021 0.002 TYR A1893 ARG 0.004 0.000 ARG A 827 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 703 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6724 (mp) REVERT: A 1346 ILE cc_start: 0.6327 (mm) cc_final: 0.5977 (mt) REVERT: A 1397 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6570 (mtm) REVERT: A 1431 LYS cc_start: 0.8149 (tttt) cc_final: 0.6958 (tmtt) REVERT: A 1455 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7211 (mt0) REVERT: A 1469 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.6111 (mtt90) REVERT: A 1476 MET cc_start: 0.7271 (mtp) cc_final: 0.6995 (mtp) REVERT: A 1531 GLU cc_start: 0.7176 (tp30) cc_final: 0.6784 (tp30) REVERT: A 1606 MET cc_start: 0.6070 (ttp) cc_final: 0.5725 (tmm) REVERT: A 1644 ILE cc_start: 0.7148 (mt) cc_final: 0.6721 (mp) REVERT: A 1651 MET cc_start: 0.5961 (mmt) cc_final: 0.5539 (mmt) outliers start: 24 outliers final: 19 residues processed: 128 average time/residue: 1.3815 time to fit residues: 193.5443 Evaluate side-chains 133 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain A residue 784 HIS Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 1058 GLN Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1200 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1384 ILE Chi-restraints excluded: chain A residue 1385 ASN Chi-restraints excluded: chain A residue 1397 MET Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1455 GLN Chi-restraints excluded: chain A residue 1469 ARG Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1573 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 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 = 0.4256 r_free = 0.4256 target = 0.202294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137946 restraints weight = 39199.891| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.18 r_work: 0.3445 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12826 Z= 0.220 Angle : 0.553 9.892 17400 Z= 0.285 Chirality : 0.039 0.188 2102 Planarity : 0.004 0.057 2313 Dihedral : 3.887 18.530 1823 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.26 % Allowed : 11.30 % 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: 3.81 (0.19), residues: 1745 helix: 3.14 (0.12), residues: 1447 sheet: 0.09 (0.73), residues: 53 loop : -1.13 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 351 HIS 0.011 0.001 HIS A 784 PHE 0.016 0.001 PHE A1390 TYR 0.021 0.002 TYR A1893 ARG 0.004 0.000 ARG A 827 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4259.94 seconds wall clock time: 77 minutes 38.47 seconds (4658.47 seconds total)