Starting phenix.real_space_refine on Sun Dec 10 06:36:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/12_2023/8tx1_41674.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/12_2023/8tx1_41674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/12_2023/8tx1_41674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/12_2023/8tx1_41674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/12_2023/8tx1_41674.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tx1_41674/12_2023/8tx1_41674.pdb" } resolution = 3.62 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= 0.002 sd= 0.092 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 83 5.16 5 C 8643 2.51 5 N 2234 2.21 5 O 2727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 953": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1187": "OE1" <-> "OE2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1239": "OE1" <-> "OE2" Residue "A TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A ASP 1342": "OD1" <-> "OD2" Residue "A TYR 1366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1393": "OE1" <-> "OE2" Residue "A PHE 1426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1507": "OD1" <-> "OD2" Residue "A PHE 1537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1575": "OD1" <-> "OD2" Residue "A TYR 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1628": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13687 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1894, 13687 Classifications: {'peptide': 1894} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 195, 'TRANS': 1694} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 7.80, per 1000 atoms: 0.57 Number of scatterers: 13687 At special positions: 0 Unit cell: (114.38, 113.05, 400.33, 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 83 16.00 O 2727 8.00 N 2234 7.00 C 8643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS A 947 " distance=2.03 Simple disulfide: pdb=" SG CYS A1052 " - pdb=" SG CYS A1110 " distance=2.05 Simple disulfide: pdb=" SG CYS A1182 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS A1216 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1247 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1287 " - pdb=" SG CYS A1301 " distance=2.03 Simple disulfide: pdb=" SG CYS A1304 " - pdb=" SG CYS A1317 " distance=2.02 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1392 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1445 " distance=2.03 Simple disulfide: pdb=" SG CYS A1448 " - pdb=" SG CYS A1462 " distance=2.03 Simple disulfide: pdb=" SG CYS A1465 " - pdb=" SG CYS A1479 " distance=2.04 Simple disulfide: pdb=" SG CYS A1482 " - pdb=" SG CYS A1546 " distance=2.03 Simple disulfide: pdb=" SG CYS A1566 " - pdb=" SG CYS A1593 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1610 " distance=2.03 Simple disulfide: pdb=" SG CYS A1613 " - pdb=" SG CYS A1627 " distance=2.03 Simple disulfide: pdb=" SG CYS A1666 " - pdb=" SG CYS A1680 " distance=2.03 Simple disulfide: pdb=" SG CYS A1683 " - pdb=" SG CYS A1697 " distance=2.03 Simple disulfide: pdb=" SG CYS A1700 " - pdb=" SG CYS A1714 " distance=2.03 Simple disulfide: pdb=" SG CYS A1717 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS A1733 " - pdb=" SG CYS A1747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1750 " - pdb=" SG CYS A1765 " distance=2.03 Simple disulfide: pdb=" SG CYS A1768 " - pdb=" SG CYS A1794 " distance=2.03 Simple disulfide: pdb=" SG CYS A1797 " - pdb=" SG CYS A1811 " distance=2.03 Simple disulfide: pdb=" SG CYS A1814 " - pdb=" SG CYS A1837 " distance=2.03 Simple disulfide: pdb=" SG CYS A1828 " - pdb=" SG CYS A1840 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.9 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 39 sheets defined 4.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 547 through 557 removed outlier: 3.580A pdb=" N TRP A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 822 through 827 removed outlier: 4.035A pdb=" N THR A 825 " --> pdb=" O ALA A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 removed outlier: 3.757A pdb=" N PHE A1077 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1424 through 1428 removed outlier: 3.638A pdb=" N THR A1428 " --> pdb=" O PRO A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1497 removed outlier: 3.601A pdb=" N MET A1497 " --> pdb=" O ARG A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1982 removed outlier: 3.772A pdb=" N GLN A1982 " --> pdb=" O ASP A1978 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.642A pdb=" N ILE A 209 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET A 189 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 311 removed outlier: 3.979A pdb=" N LEU A 363 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 372 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 391 removed outlier: 3.765A pdb=" N ILE A 403 " --> pdb=" O ASN A 453 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 405 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 451 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 423 Processing sheet with id=AA9, first strand: chain 'A' and resid 495 through 501 Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534 removed outlier: 4.073A pdb=" N GLU A 530 " --> pdb=" O ILE A 565 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 536 through 538 Processing sheet with id=AB3, first strand: chain 'A' and resid 621 through 627 Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 688 Processing sheet with id=AB5, first strand: chain 'A' and resid 751 through 758 Processing sheet with id=AB6, first strand: chain 'A' and resid 786 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 830 through 840 removed outlier: 7.036A pdb=" N ASP A 840 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 864 through 870 Processing sheet with id=AB9, first strand: chain 'A' and resid 904 through 908 Processing sheet with id=AC1, first strand: chain 'A' and resid 1006 through 1013 removed outlier: 5.899A pdb=" N VAL A1008 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A1035 " --> pdb=" O VAL A1008 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1101 removed outlier: 4.488A pdb=" N GLN A1049 " --> pdb=" O TYR A1131 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL A1128 " --> pdb=" O ASN A1139 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASN A1139 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU A1130 " --> pdb=" O GLY A1137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1187 through 1191 Processing sheet with id=AC4, first strand: chain 'A' and resid 1302 through 1303 removed outlier: 7.371A pdb=" N TYR A1291 " --> pdb=" O ALA A1314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1308 through 1309 Processing sheet with id=AC6, first strand: chain 'A' and resid 1324 through 1327 Processing sheet with id=AC7, first strand: chain 'A' and resid 1421 through 1422 removed outlier: 3.549A pdb=" N GLN A1421 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1452 through 1453 removed outlier: 3.543A pdb=" N LEU A1463 " --> pdb=" O TYR A1453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1469 through 1470 Processing sheet with id=AD1, first strand: chain 'A' and resid 1486 through 1487 Processing sheet with id=AD2, first strand: chain 'A' and resid 1570 through 1571 removed outlier: 3.703A pdb=" N TYR A1594 " --> pdb=" O PHE A1571 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1600 through 1601 Processing sheet with id=AD4, first strand: chain 'A' and resid 1617 through 1618 removed outlier: 3.597A pdb=" N GLU A1628 " --> pdb=" O PHE A1618 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1634 through 1635 removed outlier: 3.918A pdb=" N THR A1664 " --> pdb=" O PHE A1635 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1645 through 1647 Processing sheet with id=AD7, first strand: chain 'A' and resid 1670 through 1671 Processing sheet with id=AD8, first strand: chain 'A' and resid 1704 through 1705 Processing sheet with id=AD9, first strand: chain 'A' and resid 1721 through 1722 Processing sheet with id=AE1, first strand: chain 'A' and resid 1754 through 1755 removed outlier: 3.507A pdb=" N ARG A1766 " --> pdb=" O TYR A1755 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1772 through 1773 Processing sheet with id=AE3, first strand: chain 'A' and resid 1817 through 1818 275 hydrogen bonds defined for protein. 672 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: 6.09 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 1 1.16 - 1.33: 3260 1.33 - 1.50: 5227 1.50 - 1.67: 5475 1.67 - 1.84: 104 Bond restraints: 14067 Sorted by residual: bond pdb=" CB PRO A 902 " pdb=" CG PRO A 902 " ideal model delta sigma weight residual 1.492 0.991 0.501 5.00e-02 4.00e+02 1.00e+02 bond pdb=" CG PRO A 902 " pdb=" CD PRO A 902 " ideal model delta sigma weight residual 1.503 1.276 0.227 3.40e-02 8.65e+02 4.45e+01 bond pdb=" CG PRO A1528 " pdb=" CD PRO A1528 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.09e+00 bond pdb=" CB PRO A 321 " pdb=" CG PRO A 321 " ideal model delta sigma weight residual 1.492 1.621 -0.129 5.00e-02 4.00e+02 6.69e+00 bond pdb=" CB PRO A1288 " pdb=" CG PRO A1288 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 ... (remaining 14062 not shown) Histogram of bond angle deviations from ideal: 71.58 - 88.92: 2 88.92 - 106.26: 789 106.26 - 123.60: 18150 123.60 - 140.94: 451 140.94 - 158.28: 1 Bond angle restraints: 19393 Sorted by residual: angle pdb=" N PRO A 902 " pdb=" CD PRO A 902 " pdb=" CG PRO A 902 " ideal model delta sigma weight residual 103.20 74.15 29.05 1.50e+00 4.44e-01 3.75e+02 angle pdb=" CA PRO A 902 " pdb=" CB PRO A 902 " pdb=" CG PRO A 902 " ideal model delta sigma weight residual 104.50 71.58 32.92 1.90e+00 2.77e-01 3.00e+02 angle pdb=" CB PRO A 902 " pdb=" CG PRO A 902 " pdb=" CD PRO A 902 " ideal model delta sigma weight residual 106.10 158.28 -52.18 3.20e+00 9.77e-02 2.66e+02 angle pdb=" CA PRO A 902 " pdb=" N PRO A 902 " pdb=" CD PRO A 902 " ideal model delta sigma weight residual 112.00 93.50 18.50 1.40e+00 5.10e-01 1.75e+02 angle pdb=" CA PRO A 266 " pdb=" N PRO A 266 " pdb=" CD PRO A 266 " ideal model delta sigma weight residual 112.00 102.72 9.28 1.40e+00 5.10e-01 4.39e+01 ... (remaining 19388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7379 17.71 - 35.42: 843 35.42 - 53.13: 189 53.13 - 70.84: 43 70.84 - 88.55: 15 Dihedral angle restraints: 8469 sinusoidal: 3020 harmonic: 5449 Sorted by residual: dihedral pdb=" CB CYS A1750 " pdb=" SG CYS A1750 " pdb=" SG CYS A1765 " pdb=" CB CYS A1765 " ideal model delta sinusoidal sigma weight residual -86.00 -163.97 77.97 1 1.00e+01 1.00e-02 7.60e+01 dihedral pdb=" CB CYS A1320 " pdb=" SG CYS A1320 " pdb=" SG CYS A1358 " pdb=" CB CYS A1358 " ideal model delta sinusoidal sigma weight residual -86.00 -160.13 74.13 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" CB CYS A1216 " pdb=" SG CYS A1216 " pdb=" SG CYS A1228 " pdb=" CB CYS A1228 " ideal model delta sinusoidal sigma weight residual 93.00 158.21 -65.21 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1757 0.043 - 0.087: 379 0.087 - 0.130: 159 0.130 - 0.173: 7 0.173 - 0.216: 1 Chirality restraints: 2303 Sorted by residual: chirality pdb=" CA PRO A1939 " pdb=" N PRO A1939 " pdb=" C PRO A1939 " pdb=" CB PRO A1939 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A1013 " pdb=" N ILE A1013 " pdb=" C ILE A1013 " pdb=" CB ILE A1013 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA SER A1014 " pdb=" N SER A1014 " pdb=" C SER A1014 " pdb=" CB SER A1014 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 2300 not shown) Planarity restraints: 2537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 901 " 0.093 5.00e-02 4.00e+02 1.25e-01 2.50e+01 pdb=" N PRO A 902 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO A 902 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 902 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A1361 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO A1362 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO A1362 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO A1362 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 104 " -0.077 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 105 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 105 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 105 " -0.060 5.00e-02 4.00e+02 ... (remaining 2534 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 391 2.69 - 3.24: 13332 3.24 - 3.79: 20230 3.79 - 4.35: 23857 4.35 - 4.90: 39607 Nonbonded interactions: 97417 Sorted by model distance: nonbonded pdb=" OD1 ASN A1018 " pdb=" OG1 THR A1020 " model vdw 2.136 2.440 nonbonded pdb=" O PRO A1466 " pdb=" NZ LYS A1542 " model vdw 2.166 2.520 nonbonded pdb=" OG1 THR A 398 " pdb=" OD1 ASP A 400 " model vdw 2.203 2.440 nonbonded pdb=" O PRO A1484 " pdb=" OG1 THR A1555 " model vdw 2.225 2.440 nonbonded pdb=" O LYS A1567 " pdb=" OG1 THR A1570 " model vdw 2.237 2.440 ... (remaining 97412 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: 3.710 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: 11.770 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 41.470 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5104 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 : 0.006 0.501 14067 Z= 0.439 Angle : 0.922 52.177 19393 Z= 0.474 Chirality : 0.042 0.216 2303 Planarity : 0.008 0.125 2537 Dihedral : 15.941 88.553 4890 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.58 % Favored : 93.21 % Rotamer: Outliers : 0.20 % Allowed : 30.85 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.18 (0.20), residues: 1884 helix: 1.38 (0.63), residues: 68 sheet: 1.65 (0.26), residues: 395 loop : -0.42 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 420 HIS 0.002 0.001 HIS A 847 PHE 0.017 0.001 PHE A1538 TYR 0.021 0.001 TYR A1208 ARG 0.010 0.001 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 0.2202 time to fit residues: 26.5812 Evaluate side-chains 65 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1273 time to fit residues: 2.2414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 40.0000 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 148 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1058 GLN ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1637 ASN ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 14067 Z= 0.517 Angle : 0.926 12.265 19393 Z= 0.487 Chirality : 0.050 0.215 2303 Planarity : 0.009 0.110 2537 Dihedral : 6.431 40.362 2013 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.97 % Favored : 90.66 % Rotamer: Outliers : 7.12 % Allowed : 27.08 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1884 helix: -0.19 (0.59), residues: 74 sheet: 0.73 (0.26), residues: 384 loop : -1.03 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A1236 HIS 0.010 0.004 HIS A1276 PHE 0.032 0.003 PHE A1538 TYR 0.035 0.003 TYR A1453 ARG 0.013 0.001 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 70 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 47 residues processed: 166 average time/residue: 0.1971 time to fit residues: 53.2714 Evaluate side-chains 106 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 59 time to evaluate : 1.526 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.1357 time to fit residues: 13.4204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 142 optimal weight: 0.0070 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 171 optimal weight: 40.0000 chunk 185 optimal weight: 0.0040 chunk 153 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 overall best weight: 2.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14067 Z= 0.233 Angle : 0.657 8.338 19393 Z= 0.335 Chirality : 0.043 0.217 2303 Planarity : 0.006 0.082 2537 Dihedral : 5.369 36.349 2013 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.79 % Favored : 92.89 % Rotamer: Outliers : 3.09 % Allowed : 28.76 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.77 (0.19), residues: 1884 helix: 0.33 (0.61), residues: 74 sheet: 0.68 (0.26), residues: 384 loop : -0.97 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 420 HIS 0.002 0.001 HIS A1276 PHE 0.018 0.001 PHE A1538 TYR 0.013 0.001 TYR A1453 ARG 0.005 0.000 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 70 time to evaluate : 1.559 Fit side-chains outliers start: 46 outliers final: 17 residues processed: 109 average time/residue: 0.2084 time to fit residues: 37.2903 Evaluate side-chains 80 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1238 time to fit residues: 5.9778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 172 optimal weight: 0.0670 chunk 182 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14067 Z= 0.273 Angle : 0.678 9.533 19393 Z= 0.342 Chirality : 0.044 0.210 2303 Planarity : 0.006 0.078 2537 Dihedral : 5.377 33.292 2013 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.39 % Favored : 91.30 % Rotamer: Outliers : 3.70 % Allowed : 28.70 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.19), residues: 1884 helix: 0.44 (0.62), residues: 74 sheet: 0.56 (0.26), residues: 379 loop : -1.07 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 639 HIS 0.007 0.002 HIS A1276 PHE 0.018 0.002 PHE A1418 TYR 0.014 0.002 TYR A1074 ARG 0.004 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 67 time to evaluate : 1.787 Fit side-chains outliers start: 55 outliers final: 25 residues processed: 116 average time/residue: 0.1995 time to fit residues: 39.1007 Evaluate side-chains 86 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1271 time to fit residues: 8.2207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 14067 Z= 0.328 Angle : 0.724 8.584 19393 Z= 0.371 Chirality : 0.045 0.206 2303 Planarity : 0.007 0.077 2537 Dihedral : 5.726 33.617 2013 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.81 % Favored : 90.87 % Rotamer: Outliers : 3.29 % Allowed : 29.17 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.17 (0.19), residues: 1884 helix: 0.29 (0.61), residues: 74 sheet: 0.35 (0.26), residues: 377 loop : -1.25 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1397 HIS 0.009 0.003 HIS A1276 PHE 0.017 0.002 PHE A1091 TYR 0.019 0.002 TYR A1705 ARG 0.005 0.001 ARG A1359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 63 time to evaluate : 1.631 Fit side-chains outliers start: 49 outliers final: 19 residues processed: 109 average time/residue: 0.1967 time to fit residues: 37.1196 Evaluate side-chains 74 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1350 time to fit residues: 6.9037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 182 optimal weight: 30.0000 chunk 151 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14067 Z= 0.372 Angle : 0.780 10.391 19393 Z= 0.400 Chirality : 0.047 0.227 2303 Planarity : 0.007 0.084 2537 Dihedral : 6.151 34.726 2013 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.08 % Favored : 89.54 % Rotamer: Outliers : 3.49 % Allowed : 28.83 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.49 (0.19), residues: 1884 helix: 0.00 (0.60), residues: 74 sheet: 0.17 (0.27), residues: 366 loop : -1.48 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1397 HIS 0.017 0.004 HIS A1276 PHE 0.030 0.002 PHE A 662 TYR 0.022 0.002 TYR A1074 ARG 0.006 0.001 ARG A1359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 57 time to evaluate : 1.598 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 28 residues processed: 105 average time/residue: 0.2083 time to fit residues: 37.0252 Evaluate side-chains 81 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 53 time to evaluate : 1.503 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.1303 time to fit residues: 8.8202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 30.0000 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1711 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 14067 Z= 0.221 Angle : 0.654 7.794 19393 Z= 0.330 Chirality : 0.043 0.200 2303 Planarity : 0.006 0.082 2537 Dihedral : 5.523 30.030 2013 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.86 % Favored : 91.83 % Rotamer: Outliers : 1.48 % Allowed : 30.04 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 1884 helix: 0.39 (0.62), residues: 74 sheet: 0.16 (0.27), residues: 366 loop : -1.31 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1397 HIS 0.007 0.002 HIS A1276 PHE 0.014 0.001 PHE A 172 TYR 0.018 0.001 TYR A1029 ARG 0.005 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 1.544 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 78 average time/residue: 0.2065 time to fit residues: 27.4113 Evaluate side-chains 62 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1272 time to fit residues: 4.9558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 0.3980 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14067 Z= 0.200 Angle : 0.624 7.506 19393 Z= 0.312 Chirality : 0.042 0.188 2303 Planarity : 0.006 0.078 2537 Dihedral : 5.123 25.238 2013 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.97 % Favored : 90.76 % Rotamer: Outliers : 0.81 % Allowed : 30.71 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1884 helix: 0.51 (0.62), residues: 74 sheet: 0.26 (0.28), residues: 366 loop : -1.21 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1397 HIS 0.007 0.002 HIS A1276 PHE 0.012 0.001 PHE A 611 TYR 0.012 0.001 TYR A1366 ARG 0.004 0.000 ARG A1712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 1.519 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 0.2195 time to fit residues: 24.6105 Evaluate side-chains 57 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 1.506 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1284 time to fit residues: 3.7328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 14067 Z= 0.458 Angle : 0.849 14.364 19393 Z= 0.441 Chirality : 0.049 0.251 2303 Planarity : 0.008 0.093 2537 Dihedral : 6.611 37.380 2013 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 25.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.78 % Favored : 87.90 % Rotamer: Outliers : 0.81 % Allowed : 30.98 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.12 % 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: -1.74 (0.19), residues: 1884 helix: -0.46 (0.59), residues: 75 sheet: -0.31 (0.27), residues: 378 loop : -1.55 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A1236 HIS 0.023 0.005 HIS A1276 PHE 0.028 0.003 PHE A 662 TYR 0.032 0.003 TYR A1366 ARG 0.011 0.001 ARG A1242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 1.603 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 0.2217 time to fit residues: 25.3021 Evaluate side-chains 57 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1304 time to fit residues: 3.6468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 173 optimal weight: 50.0000 chunk 149 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 159 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5616 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14067 Z= 0.216 Angle : 0.656 7.940 19393 Z= 0.331 Chirality : 0.043 0.208 2303 Planarity : 0.006 0.083 2537 Dihedral : 5.537 27.912 2013 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.23 % Favored : 91.45 % Rotamer: Outliers : 0.20 % Allowed : 31.05 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1884 helix: 0.15 (0.61), residues: 74 sheet: -0.14 (0.28), residues: 364 loop : -1.30 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1417 HIS 0.009 0.003 HIS A 847 PHE 0.015 0.001 PHE A 833 TYR 0.014 0.001 TYR A1325 ARG 0.006 0.001 ARG A1242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.500 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 60 average time/residue: 0.2294 time to fit residues: 23.0835 Evaluate side-chains 52 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 1.534 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1257 time to fit residues: 2.5080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.133694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.120563 restraints weight = 93231.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.119622 restraints weight = 86461.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.120011 restraints weight = 66858.238| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14067 Z= 0.248 Angle : 0.670 9.336 19393 Z= 0.336 Chirality : 0.043 0.202 2303 Planarity : 0.007 0.085 2537 Dihedral : 5.480 29.964 2013 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.19 % Favored : 89.49 % Rotamer: Outliers : 0.20 % Allowed : 31.52 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.01 % 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: -1.40 (0.20), residues: 1884 helix: 0.28 (0.61), residues: 74 sheet: -0.10 (0.28), residues: 368 loop : -1.32 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 771 HIS 0.009 0.003 HIS A1276 PHE 0.014 0.001 PHE A 611 TYR 0.014 0.001 TYR A1206 ARG 0.005 0.001 ARG A1712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2415.73 seconds wall clock time: 45 minutes 16.10 seconds (2716.10 seconds total)