Starting phenix.real_space_refine on Sun May 18 02:41:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hai_34591/05_2025/8hai_34591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hai_34591/05_2025/8hai_34591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hai_34591/05_2025/8hai_34591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hai_34591/05_2025/8hai_34591.map" model { file = "/net/cci-nas-00/data/ceres_data/8hai_34591/05_2025/8hai_34591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hai_34591/05_2025/8hai_34591.cif" } resolution = 4.7 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= 0.003 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 47 5.16 5 C 9542 2.51 5 N 3017 2.21 5 O 3647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16547 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'HIS:plan': 1, 'ALY:plan-2': 2, 'ALY:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 801 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 4381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4381 Classifications: {'peptide': 533} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 497} Chain breaks: 2 Chain: "J" Number of atoms: 3012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3012 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3015 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 9.25, per 1000 atoms: 0.56 Number of scatterers: 16547 At special positions: 0 Unit cell: (107.31, 167.58, 138.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 294 15.00 O 3647 8.00 N 3017 7.00 C 9542 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: 4.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 61.3% alpha, 7.2% beta 112 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 6.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.540A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.594A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.766A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.637A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.394A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.582A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.560A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.587A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.677A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.407A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.658A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 1052 through 1067 Proline residue: K1060 - end of helix Processing helix chain 'K' and resid 1072 through 1076 Processing helix chain 'K' and resid 1080 through 1085 Processing helix chain 'K' and resid 1088 through 1093 Processing helix chain 'K' and resid 1098 through 1108 Processing helix chain 'K' and resid 1113 through 1132 removed outlier: 4.212A pdb=" N TYR K1117 " --> pdb=" O GLU K1113 " (cutoff:3.500A) Processing helix chain 'K' and resid 1136 through 1160 removed outlier: 3.543A pdb=" N LYS K1140 " --> pdb=" O SER K1136 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix Processing helix chain 'K' and resid 1256 through 1260 Processing helix chain 'K' and resid 1272 through 1279 Processing helix chain 'K' and resid 1296 through 1314 Processing helix chain 'K' and resid 1336 through 1343 Processing helix chain 'K' and resid 1406 through 1429 removed outlier: 4.225A pdb=" N THR K1411 " --> pdb=" O LYS K1407 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA K1412 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY K1420 " --> pdb=" O GLU K1416 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS K1426 " --> pdb=" O LEU K1422 " (cutoff:3.500A) Processing helix chain 'K' and resid 1459 through 1477 Processing helix chain 'K' and resid 1486 through 1493 Processing helix chain 'K' and resid 1497 through 1501 removed outlier: 3.582A pdb=" N LEU K1501 " --> pdb=" O ALA K1498 " (cutoff:3.500A) Processing helix chain 'K' and resid 1507 through 1523 removed outlier: 3.963A pdb=" N ASN K1511 " --> pdb=" O ASP K1507 " (cutoff:3.500A) Processing helix chain 'K' and resid 1579 through 1591 Processing helix chain 'K' and resid 1602 through 1607 removed outlier: 4.200A pdb=" N ALA K1605 " --> pdb=" O ALA K1602 " (cutoff:3.500A) Processing helix chain 'K' and resid 1621 through 1625 Processing helix chain 'K' and resid 1627 through 1638 Processing helix chain 'K' and resid 1643 through 1663 removed outlier: 3.588A pdb=" N GLN K1663 " --> pdb=" O HIS K1659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.644A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.588A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.510A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.188A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.849A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.194A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 1169 through 1170 removed outlier: 3.736A pdb=" N ASP K1240 " --> pdb=" O PHE K1170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1198 through 1200 Processing sheet with id=AB4, first strand: chain 'K' and resid 1244 through 1246 Processing sheet with id=AB5, first strand: chain 'K' and resid 1321 through 1334 removed outlier: 6.465A pdb=" N ALA K1359 " --> pdb=" O VAL K1326 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA K1328 " --> pdb=" O THR K1357 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR K1357 " --> pdb=" O ALA K1328 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP K1330 " --> pdb=" O TYR K1355 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR K1355 " --> pdb=" O ASP K1330 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR K1332 " --> pdb=" O PHE K1353 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE K1353 " --> pdb=" O THR K1332 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU K1360 " --> pdb=" O MET K1376 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE K1374 " --> pdb=" O ALA K1362 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU K1364 " --> pdb=" O CYS K1372 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N CYS K1372 " --> pdb=" O GLU K1364 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE K1366 " --> pdb=" O ASP K1370 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP K1370 " --> pdb=" O ILE K1366 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN K1379 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ILE K1395 " --> pdb=" O GLN K1379 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR K1381 " --> pdb=" O VAL K1393 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL K1393 " --> pdb=" O TYR K1381 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP K1482 " --> pdb=" O ARG K1599 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 266 hydrogen bonds 532 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 8.02 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3938 1.34 - 1.46: 4891 1.46 - 1.58: 7993 1.58 - 1.70: 586 1.70 - 1.82: 70 Bond restraints: 17478 Sorted by residual: bond pdb=" NZ ALY B 16 " pdb=" CH ALY B 16 " ideal model delta sigma weight residual 1.343 1.385 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.326 1.351 -0.024 1.84e-02 2.95e+03 1.76e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CH ALY B 16 " pdb=" OH ALY B 16 " ideal model delta sigma weight residual 1.225 1.247 -0.022 2.00e-02 2.50e+03 1.23e+00 ... (remaining 17473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 24227 1.64 - 3.28: 596 3.28 - 4.92: 32 4.92 - 6.56: 11 6.56 - 8.20: 3 Bond angle restraints: 24869 Sorted by residual: angle pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta sigma weight residual 122.97 119.57 3.40 9.80e-01 1.04e+00 1.20e+01 angle pdb=" N ILE K1479 " pdb=" CA ILE K1479 " pdb=" C ILE K1479 " ideal model delta sigma weight residual 111.45 108.33 3.12 9.30e-01 1.16e+00 1.12e+01 angle pdb=" CB MET H 62 " pdb=" CG MET H 62 " pdb=" SD MET H 62 " ideal model delta sigma weight residual 112.70 120.90 -8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" CA ARG K1494 " pdb=" CB ARG K1494 " pdb=" CG ARG K1494 " ideal model delta sigma weight residual 114.10 119.37 -5.27 2.00e+00 2.50e-01 6.93e+00 angle pdb=" CB ARG E 52 " pdb=" CG ARG E 52 " pdb=" CD ARG E 52 " ideal model delta sigma weight residual 111.30 117.32 -6.02 2.30e+00 1.89e-01 6.85e+00 ... (remaining 24864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 8559 35.34 - 70.67: 1299 70.67 - 106.01: 22 106.01 - 141.34: 0 141.34 - 176.68: 2 Dihedral angle restraints: 9882 sinusoidal: 6059 harmonic: 3823 Sorted by residual: dihedral pdb=" C4' DT I 136 " pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " pdb=" P DT I 137 " ideal model delta sinusoidal sigma weight residual -140.00 36.68 -176.68 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA J 59 " pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " pdb=" P DA J 60 " ideal model delta sinusoidal sigma weight residual 220.00 53.71 166.29 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual 180.00 -163.72 -16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 9879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1895 0.028 - 0.055: 612 0.055 - 0.082: 168 0.082 - 0.110: 70 0.110 - 0.137: 27 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CA TYR B 88 " pdb=" N TYR B 88 " pdb=" C TYR B 88 " pdb=" CB TYR B 88 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ILE K1598 " pdb=" N ILE K1598 " pdb=" C ILE K1598 " pdb=" CB ILE K1598 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA ILE F 46 " pdb=" N ILE F 46 " pdb=" C ILE F 46 " pdb=" CB ILE F 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 2769 not shown) Planarity restraints: 2150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.020 2.00e-02 2.50e+03 1.63e-02 5.31e+00 pdb=" CG TYR B 88 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LYS B 59 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS B 59 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL B 60 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO D 103 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.022 5.00e-02 4.00e+02 ... (remaining 2147 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2774 2.78 - 3.31: 16057 3.31 - 3.84: 32438 3.84 - 4.37: 36547 4.37 - 4.90: 53996 Nonbonded interactions: 141812 Sorted by model distance: nonbonded pdb=" NH1 ARG C 29 " pdb=" O SER D 36 " model vdw 2.249 3.120 nonbonded pdb=" N GLN G 24 " pdb=" OE2 GLU G 56 " model vdw 2.264 3.120 nonbonded pdb=" N THR H 90 " pdb=" OE2 GLU H 93 " model vdw 2.277 3.120 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.286 3.120 nonbonded pdb=" O TYR B 51 " pdb=" OG1 THR B 54 " model vdw 2.309 3.040 ... (remaining 141807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 19 through 101) selection = (chain 'F' and (resid 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 101)) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 124) } ncs_group { reference = (chain 'I' and resid 18 through 163) selection = (chain 'J' and resid 18 through 163) } 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=0.00 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: 0.700 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 42.810 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.540 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.003 0.042 17478 Z= 0.146 Angle : 0.578 8.197 24869 Z= 0.359 Chirality : 0.033 0.137 2772 Planarity : 0.004 0.039 2150 Dihedral : 24.523 176.680 7414 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.74 (0.24), residues: 1283 helix: 1.61 (0.19), residues: 777 sheet: 0.55 (0.65), residues: 68 loop : 0.60 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1509 HIS 0.004 0.000 HIS A 39 PHE 0.011 0.001 PHE G 25 TYR 0.039 0.001 TYR B 88 ARG 0.006 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.12563 ( 860) hydrogen bonds : angle 5.03596 ( 2278) covalent geometry : bond 0.00282 (17478) covalent geometry : angle 0.57781 (24869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9049 (m-30) cc_final: 0.8814 (m-30) REVERT: D 100 LEU cc_start: 0.9459 (mt) cc_final: 0.9232 (mt) REVERT: G 73 ASN cc_start: 0.8705 (t0) cc_final: 0.8365 (t0) REVERT: K 1094 LYS cc_start: 0.7492 (mtpt) cc_final: 0.6648 (mmmt) REVERT: K 1097 MET cc_start: 0.3272 (ppp) cc_final: 0.2525 (tmm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2716 time to fit residues: 43.0281 Evaluate side-chains 67 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 64 ASN C 104 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN K1112 GLN K1255 HIS K1379 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.055556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.039725 restraints weight = 175666.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040460 restraints weight = 109201.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040277 restraints weight = 86716.357| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17478 Z= 0.250 Angle : 0.673 8.055 24869 Z= 0.380 Chirality : 0.039 0.143 2772 Planarity : 0.006 0.052 2150 Dihedral : 28.775 169.701 4768 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.86 (0.23), residues: 1283 helix: 1.78 (0.18), residues: 775 sheet: 0.43 (0.68), residues: 64 loop : 0.52 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1509 HIS 0.009 0.001 HIS B 75 PHE 0.018 0.002 PHE G 25 TYR 0.035 0.002 TYR B 88 ARG 0.008 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.07066 ( 860) hydrogen bonds : angle 3.63730 ( 2278) covalent geometry : bond 0.00540 (17478) covalent geometry : angle 0.67312 (24869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 1.475 Fit side-chains REVERT: A 120 MET cc_start: 0.8320 (mpp) cc_final: 0.7902 (mpp) REVERT: B 68 ASP cc_start: 0.9392 (m-30) cc_final: 0.9004 (m-30) REVERT: B 88 TYR cc_start: 0.8534 (m-80) cc_final: 0.8283 (m-80) REVERT: D 45 LEU cc_start: 0.8981 (tp) cc_final: 0.8774 (tp) REVERT: D 54 ILE cc_start: 0.8814 (pt) cc_final: 0.8553 (mm) REVERT: D 100 LEU cc_start: 0.9244 (mt) cc_final: 0.9019 (mt) REVERT: E 73 GLU cc_start: 0.8685 (tt0) cc_final: 0.8348 (mt-10) REVERT: E 120 MET cc_start: 0.8532 (mtm) cc_final: 0.8005 (ptp) REVERT: G 38 ASN cc_start: 0.8447 (m-40) cc_final: 0.7577 (m-40) REVERT: G 41 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8093 (tm-30) REVERT: G 73 ASN cc_start: 0.8871 (t0) cc_final: 0.8465 (t0) REVERT: H 46 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8544 (pttm) REVERT: H 69 ILE cc_start: 0.9172 (mm) cc_final: 0.8928 (mm) REVERT: K 1090 PHE cc_start: 0.8542 (m-10) cc_final: 0.7906 (m-80) REVERT: K 1094 LYS cc_start: 0.7611 (mtpt) cc_final: 0.7122 (mmmt) REVERT: K 1097 MET cc_start: 0.3002 (ppp) cc_final: 0.2589 (ppp) REVERT: K 1349 MET cc_start: 0.0635 (mmt) cc_final: 0.0260 (mtt) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.2576 time to fit residues: 36.9741 Evaluate side-chains 63 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 0 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 112 optimal weight: 0.0470 chunk 82 optimal weight: 0.2980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 108 ASN B 64 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.058987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.043064 restraints weight = 185497.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.044136 restraints weight = 107026.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.044819 restraints weight = 74490.579| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17478 Z= 0.136 Angle : 0.539 7.129 24869 Z= 0.313 Chirality : 0.034 0.179 2772 Planarity : 0.004 0.037 2150 Dihedral : 28.773 179.898 4768 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.09 % Allowed : 2.23 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 2.18 (0.23), residues: 1283 helix: 2.07 (0.18), residues: 783 sheet: 0.43 (0.68), residues: 64 loop : 0.59 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1509 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE G 25 TYR 0.017 0.001 TYR G 50 ARG 0.013 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 860) hydrogen bonds : angle 3.12673 ( 2278) covalent geometry : bond 0.00290 (17478) covalent geometry : angle 0.53936 (24869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8884 (tt0) cc_final: 0.8343 (pt0) REVERT: A 105 GLU cc_start: 0.8987 (tp30) cc_final: 0.8590 (tp30) REVERT: A 120 MET cc_start: 0.8263 (mpp) cc_final: 0.7867 (mpp) REVERT: B 63 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: B 68 ASP cc_start: 0.9226 (m-30) cc_final: 0.8770 (m-30) REVERT: B 88 TYR cc_start: 0.8559 (m-10) cc_final: 0.8282 (m-80) REVERT: E 73 GLU cc_start: 0.8739 (tt0) cc_final: 0.8357 (mt-10) REVERT: G 41 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8028 (tm-30) REVERT: G 73 ASN cc_start: 0.8902 (t0) cc_final: 0.8561 (t0) REVERT: H 46 LYS cc_start: 0.9172 (mmpt) cc_final: 0.8447 (pttm) REVERT: H 69 ILE cc_start: 0.9190 (mm) cc_final: 0.8928 (mm) REVERT: K 1090 PHE cc_start: 0.8490 (m-10) cc_final: 0.7819 (m-80) REVERT: K 1094 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7193 (mmmt) REVERT: K 1349 MET cc_start: 0.1663 (mmt) cc_final: 0.1290 (mtt) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.2641 time to fit residues: 40.3905 Evaluate side-chains 67 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 105 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN K1262 HIS K1451 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.053231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.036917 restraints weight = 180352.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.037870 restraints weight = 105860.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.038468 restraints weight = 75341.790| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17478 Z= 0.231 Angle : 0.633 6.855 24869 Z= 0.361 Chirality : 0.037 0.160 2772 Planarity : 0.005 0.059 2150 Dihedral : 29.151 176.381 4768 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 2.09 (0.23), residues: 1283 helix: 2.01 (0.18), residues: 770 sheet: 0.94 (0.76), residues: 58 loop : 0.47 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1509 HIS 0.007 0.001 HIS B 75 PHE 0.014 0.002 PHE B 61 TYR 0.018 0.002 TYR F 88 ARG 0.009 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.06825 ( 860) hydrogen bonds : angle 3.46368 ( 2278) covalent geometry : bond 0.00501 (17478) covalent geometry : angle 0.63279 (24869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.738 Fit side-chains REVERT: A 120 MET cc_start: 0.8385 (mpp) cc_final: 0.8036 (mpp) REVERT: B 68 ASP cc_start: 0.9400 (m-30) cc_final: 0.8866 (m-30) REVERT: D 93 GLU cc_start: 0.9124 (mp0) cc_final: 0.8513 (mp0) REVERT: E 120 MET cc_start: 0.8746 (mtm) cc_final: 0.7974 (mtp) REVERT: G 38 ASN cc_start: 0.8520 (m-40) cc_final: 0.7947 (m-40) REVERT: G 73 ASN cc_start: 0.8938 (t0) cc_final: 0.8612 (t0) REVERT: H 69 ILE cc_start: 0.9238 (mm) cc_final: 0.8976 (mm) REVERT: K 1090 PHE cc_start: 0.8571 (m-10) cc_final: 0.7960 (m-80) REVERT: K 1094 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7407 (mmmt) REVERT: K 1349 MET cc_start: 0.1243 (mmt) cc_final: 0.0418 (mtt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2612 time to fit residues: 33.7065 Evaluate side-chains 57 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.054853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039058 restraints weight = 190866.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040182 restraints weight = 104668.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.040866 restraints weight = 70559.570| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17478 Z= 0.174 Angle : 0.580 6.136 24869 Z= 0.334 Chirality : 0.035 0.152 2772 Planarity : 0.004 0.038 2150 Dihedral : 29.309 179.870 4768 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 2.08 (0.23), residues: 1283 helix: 1.98 (0.18), residues: 782 sheet: 0.79 (0.73), residues: 62 loop : 0.50 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1509 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE G 25 TYR 0.032 0.002 TYR F 88 ARG 0.006 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 860) hydrogen bonds : angle 3.29241 ( 2278) covalent geometry : bond 0.00374 (17478) covalent geometry : angle 0.57986 (24869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.372 Fit side-chains REVERT: A 105 GLU cc_start: 0.8875 (tp30) cc_final: 0.8484 (tp30) REVERT: A 120 MET cc_start: 0.8377 (mpp) cc_final: 0.8016 (mpp) REVERT: B 68 ASP cc_start: 0.9439 (m-30) cc_final: 0.8940 (m-30) REVERT: D 93 GLU cc_start: 0.9113 (mp0) cc_final: 0.8669 (mp0) REVERT: D 100 LEU cc_start: 0.8918 (mt) cc_final: 0.8714 (mt) REVERT: E 120 MET cc_start: 0.8794 (mtm) cc_final: 0.8011 (mtp) REVERT: G 38 ASN cc_start: 0.7890 (m-40) cc_final: 0.7649 (m-40) REVERT: G 73 ASN cc_start: 0.9012 (t0) cc_final: 0.8767 (t0) REVERT: H 69 ILE cc_start: 0.9310 (mm) cc_final: 0.9065 (mm) REVERT: K 1090 PHE cc_start: 0.8571 (m-10) cc_final: 0.7978 (m-80) REVERT: K 1094 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7555 (mmmt) REVERT: K 1349 MET cc_start: 0.2468 (mmt) cc_final: 0.1791 (mtt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2610 time to fit residues: 34.3287 Evaluate side-chains 59 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1489 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 = 0.3471 r_free = 0.3471 target = 0.053637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.037960 restraints weight = 192491.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039050 restraints weight = 105737.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039752 restraints weight = 71524.140| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17478 Z= 0.190 Angle : 0.584 6.223 24869 Z= 0.338 Chirality : 0.035 0.152 2772 Planarity : 0.004 0.039 2150 Dihedral : 29.353 177.931 4768 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.97 (0.23), residues: 1283 helix: 1.90 (0.18), residues: 788 sheet: 0.89 (0.76), residues: 58 loop : 0.38 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1509 HIS 0.006 0.001 HIS H 82 PHE 0.010 0.001 PHE E 67 TYR 0.034 0.002 TYR B 88 ARG 0.007 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 860) hydrogen bonds : angle 3.29196 ( 2278) covalent geometry : bond 0.00409 (17478) covalent geometry : angle 0.58384 (24869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8938 (tp30) cc_final: 0.8540 (tp30) REVERT: A 120 MET cc_start: 0.8443 (mpp) cc_final: 0.8030 (mpp) REVERT: B 68 ASP cc_start: 0.9481 (m-30) cc_final: 0.8984 (m-30) REVERT: C 90 ASP cc_start: 0.8874 (t0) cc_final: 0.8617 (t0) REVERT: D 93 GLU cc_start: 0.9152 (mp0) cc_final: 0.8536 (mp0) REVERT: E 120 MET cc_start: 0.8856 (mtm) cc_final: 0.8046 (mtp) REVERT: G 73 ASN cc_start: 0.8973 (t0) cc_final: 0.8727 (t0) REVERT: H 69 ILE cc_start: 0.9305 (mm) cc_final: 0.9089 (mm) REVERT: K 1090 PHE cc_start: 0.8685 (m-10) cc_final: 0.8161 (m-80) REVERT: K 1094 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7874 (mmmt) REVERT: K 1349 MET cc_start: 0.3697 (mmt) cc_final: 0.2936 (mtt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2421 time to fit residues: 30.9642 Evaluate side-chains 55 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 82 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 108 ASN C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN K1255 HIS ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1415 HIS K1449 HIS ** K1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.048379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032685 restraints weight = 187084.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033562 restraints weight = 111164.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.034116 restraints weight = 79590.719| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17478 Z= 0.330 Angle : 0.760 9.182 24869 Z= 0.427 Chirality : 0.041 0.238 2772 Planarity : 0.006 0.076 2150 Dihedral : 30.195 179.211 4768 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.18 % Allowed : 2.14 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.02 (0.22), residues: 1283 helix: 1.18 (0.18), residues: 773 sheet: 0.50 (0.75), residues: 56 loop : -0.03 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K1509 HIS 0.007 0.002 HIS B 75 PHE 0.026 0.002 PHE C 25 TYR 0.053 0.003 TYR B 88 ARG 0.012 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.08736 ( 860) hydrogen bonds : angle 4.16878 ( 2278) covalent geometry : bond 0.00715 (17478) covalent geometry : angle 0.75982 (24869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8653 (tp30) cc_final: 0.8292 (tp30) REVERT: A 120 MET cc_start: 0.8519 (mpp) cc_final: 0.8151 (mpp) REVERT: B 68 ASP cc_start: 0.9728 (m-30) cc_final: 0.9438 (m-30) REVERT: D 59 MET cc_start: 0.9087 (tpt) cc_final: 0.8830 (tpp) REVERT: D 100 LEU cc_start: 0.8941 (mt) cc_final: 0.8724 (mt) REVERT: E 120 MET cc_start: 0.9083 (mtm) cc_final: 0.8293 (mtp) REVERT: F 88 TYR cc_start: 0.8297 (m-80) cc_final: 0.8050 (m-80) REVERT: G 38 ASN cc_start: 0.8769 (m110) cc_final: 0.8219 (m-40) REVERT: H 69 ILE cc_start: 0.9307 (mm) cc_final: 0.9084 (mm) REVERT: K 1097 MET cc_start: 0.1424 (ppp) cc_final: 0.0345 (ptt) REVERT: K 1349 MET cc_start: 0.3714 (mmt) cc_final: 0.2862 (mtp) outliers start: 2 outliers final: 0 residues processed: 73 average time/residue: 0.2624 time to fit residues: 31.4121 Evaluate side-chains 48 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 132 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 115 optimal weight: 0.3980 chunk 126 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN K1132 ASN ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1659 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.050487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.034530 restraints weight = 182678.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.035490 restraints weight = 106650.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036091 restraints weight = 75444.726| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17478 Z= 0.165 Angle : 0.613 7.831 24869 Z= 0.349 Chirality : 0.036 0.160 2772 Planarity : 0.004 0.054 2150 Dihedral : 29.973 176.741 4768 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.58 (0.23), residues: 1283 helix: 1.69 (0.18), residues: 785 sheet: 0.67 (0.76), residues: 55 loop : 0.04 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K1266 HIS 0.009 0.001 HIS K1415 PHE 0.040 0.001 PHE K1075 TYR 0.040 0.002 TYR B 88 ARG 0.006 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 860) hydrogen bonds : angle 3.46577 ( 2278) covalent geometry : bond 0.00357 (17478) covalent geometry : angle 0.61335 (24869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.522 Fit side-chains REVERT: A 105 GLU cc_start: 0.8715 (tp30) cc_final: 0.8350 (tp30) REVERT: A 120 MET cc_start: 0.8477 (mpp) cc_final: 0.8166 (mpp) REVERT: B 68 ASP cc_start: 0.9401 (m-30) cc_final: 0.8927 (m-30) REVERT: D 93 GLU cc_start: 0.9181 (mp0) cc_final: 0.8774 (mp0) REVERT: E 81 ASP cc_start: 0.8492 (t70) cc_final: 0.8182 (t0) REVERT: E 120 MET cc_start: 0.8994 (mtm) cc_final: 0.8210 (mtp) REVERT: F 88 TYR cc_start: 0.8068 (m-80) cc_final: 0.7767 (m-10) REVERT: G 73 ASN cc_start: 0.8746 (t0) cc_final: 0.8454 (t0) REVERT: H 69 ILE cc_start: 0.9345 (mm) cc_final: 0.9125 (mm) REVERT: K 1075 PHE cc_start: 0.9379 (t80) cc_final: 0.9171 (t80) REVERT: K 1097 MET cc_start: 0.1454 (ppp) cc_final: 0.0334 (ptt) REVERT: K 1254 MET cc_start: 0.0762 (ttt) cc_final: -0.0850 (mmm) REVERT: K 1314 ASN cc_start: 0.7307 (t0) cc_final: 0.6898 (m110) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2359 time to fit residues: 30.7909 Evaluate side-chains 52 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 116 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.049912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.034022 restraints weight = 184718.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035002 restraints weight = 106557.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.035602 restraints weight = 74943.749| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17478 Z= 0.189 Angle : 0.620 9.099 24869 Z= 0.353 Chirality : 0.036 0.156 2772 Planarity : 0.004 0.047 2150 Dihedral : 29.850 178.670 4768 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.65 (0.23), residues: 1283 helix: 1.79 (0.18), residues: 782 sheet: 0.54 (0.76), residues: 56 loop : 0.01 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1509 HIS 0.010 0.001 HIS K1415 PHE 0.030 0.002 PHE A 104 TYR 0.041 0.002 TYR B 88 ARG 0.009 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.05445 ( 860) hydrogen bonds : angle 3.53812 ( 2278) covalent geometry : bond 0.00410 (17478) covalent geometry : angle 0.62045 (24869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8722 (tp30) cc_final: 0.8377 (tp30) REVERT: B 68 ASP cc_start: 0.9439 (m-30) cc_final: 0.9039 (m-30) REVERT: D 93 GLU cc_start: 0.9225 (mp0) cc_final: 0.8681 (mp0) REVERT: D 100 LEU cc_start: 0.8829 (mt) cc_final: 0.8620 (mt) REVERT: E 81 ASP cc_start: 0.8582 (t70) cc_final: 0.8278 (t0) REVERT: E 120 MET cc_start: 0.9036 (mtm) cc_final: 0.8241 (mtp) REVERT: F 88 TYR cc_start: 0.8062 (m-80) cc_final: 0.7714 (m-10) REVERT: G 73 ASN cc_start: 0.8792 (t0) cc_final: 0.8509 (t0) REVERT: H 69 ILE cc_start: 0.9303 (mm) cc_final: 0.9087 (mm) REVERT: K 1075 PHE cc_start: 0.9371 (t80) cc_final: 0.9156 (t80) REVERT: K 1097 MET cc_start: 0.1688 (ppp) cc_final: 0.0955 (ppp) REVERT: K 1254 MET cc_start: 0.1339 (ttt) cc_final: -0.0125 (mmp) REVERT: K 1349 MET cc_start: 0.2883 (mtt) cc_final: 0.2325 (mtt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2285 time to fit residues: 28.4401 Evaluate side-chains 52 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K1262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.050637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034827 restraints weight = 185742.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.035798 restraints weight = 108259.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.036411 restraints weight = 76429.275| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17478 Z= 0.162 Angle : 0.593 7.750 24869 Z= 0.338 Chirality : 0.036 0.149 2772 Planarity : 0.004 0.043 2150 Dihedral : 29.715 176.558 4768 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.77 (0.23), residues: 1283 helix: 1.91 (0.18), residues: 782 sheet: 0.47 (0.74), residues: 61 loop : 0.02 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1509 HIS 0.010 0.001 HIS K1415 PHE 0.021 0.001 PHE A 104 TYR 0.038 0.002 TYR B 88 ARG 0.010 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 860) hydrogen bonds : angle 3.39682 ( 2278) covalent geometry : bond 0.00349 (17478) covalent geometry : angle 0.59291 (24869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 104 PHE cc_start: 0.9367 (m-80) cc_final: 0.8994 (m-10) REVERT: A 105 GLU cc_start: 0.8620 (tp30) cc_final: 0.8351 (tp30) REVERT: B 68 ASP cc_start: 0.9411 (m-30) cc_final: 0.8956 (m-30) REVERT: D 93 GLU cc_start: 0.9202 (mp0) cc_final: 0.8601 (mp0) REVERT: E 81 ASP cc_start: 0.8530 (t70) cc_final: 0.8227 (t0) REVERT: E 120 MET cc_start: 0.8916 (mtm) cc_final: 0.8218 (mtp) REVERT: F 88 TYR cc_start: 0.7904 (m-80) cc_final: 0.7556 (m-10) REVERT: G 73 ASN cc_start: 0.8820 (t0) cc_final: 0.8583 (t0) REVERT: K 1097 MET cc_start: 0.1635 (ppp) cc_final: 0.1092 (ppp) REVERT: K 1254 MET cc_start: 0.1234 (ttt) cc_final: -0.0133 (mmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2310 time to fit residues: 30.0293 Evaluate side-chains 52 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 120 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 107 optimal weight: 0.0370 chunk 30 optimal weight: 0.4980 chunk 151 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 20.0000 overall best weight: 3.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN E 39 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1199 HIS ** K1255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.049032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.034301 restraints weight = 186881.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034500 restraints weight = 114689.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.034919 restraints weight = 87200.469| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17478 Z= 0.242 Angle : 0.652 7.786 24869 Z= 0.369 Chirality : 0.037 0.147 2772 Planarity : 0.005 0.050 2150 Dihedral : 29.974 178.383 4768 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.63 (0.23), residues: 1283 helix: 1.84 (0.18), residues: 769 sheet: 0.38 (0.77), residues: 56 loop : -0.06 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K1509 HIS 0.009 0.001 HIS K1415 PHE 0.024 0.002 PHE E 67 TYR 0.038 0.002 TYR B 88 ARG 0.008 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.06385 ( 860) hydrogen bonds : angle 3.72791 ( 2278) covalent geometry : bond 0.00522 (17478) covalent geometry : angle 0.65156 (24869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4722.19 seconds wall clock time: 83 minutes 34.17 seconds (5014.17 seconds total)