Starting phenix.real_space_refine on Mon Nov 18 13:27:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/11_2024/8hal_34595.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/11_2024/8hal_34595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/11_2024/8hal_34595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/11_2024/8hal_34595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/11_2024/8hal_34595.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hal_34595/11_2024/8hal_34595.cif" } resolution = 4.4 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 302 5.49 5 S 46 5.16 5 C 9551 2.51 5 N 3022 2.21 5 O 3664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16585 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: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 728 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 764 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3094 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3097 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "K" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4238 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 481} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 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: 9.58, per 1000 atoms: 0.58 Number of scatterers: 16585 At special positions: 0 Unit cell: (110.25, 170.52, 136.71, 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 46 16.00 P 302 15.00 O 3664 8.00 N 3022 7.00 C 9551 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: 4.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 61.0% alpha, 6.8% beta 117 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 7.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.730A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.666A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.124A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.289A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.543A 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: 3.504A 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 removed outlier: 3.948A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.605A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.078A 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 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: 4.376A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.742A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.684A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 1087 through 1104 Proline residue: K1096 - end of helix removed outlier: 3.657A pdb=" N GLN K1104 " --> pdb=" O ALA K1100 " (cutoff:3.500A) Processing helix chain 'K' and resid 1108 through 1112 Processing helix chain 'K' and resid 1116 through 1121 Processing helix chain 'K' and resid 1124 through 1129 Processing helix chain 'K' and resid 1134 through 1144 Processing helix chain 'K' and resid 1150 through 1168 Processing helix chain 'K' and resid 1172 through 1195 removed outlier: 3.711A pdb=" N LYS K1176 " --> pdb=" O SER K1172 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP K1190 " --> pdb=" O GLU K1186 " (cutoff:3.500A) Proline residue: K1191 - end of helix removed outlier: 3.762A pdb=" N SER K1195 " --> pdb=" O PRO K1191 " (cutoff:3.500A) Processing helix chain 'K' and resid 1292 through 1296 Processing helix chain 'K' and resid 1308 through 1314 Processing helix chain 'K' and resid 1332 through 1350 Processing helix chain 'K' and resid 1372 through 1380 Processing helix chain 'K' and resid 1442 through 1465 removed outlier: 4.135A pdb=" N THR K1447 " --> pdb=" O ARG K1443 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA K1448 " --> pdb=" O CYS K1444 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU K1452 " --> pdb=" O ALA K1448 " (cutoff:3.500A) Processing helix chain 'K' and resid 1495 through 1513 Processing helix chain 'K' and resid 1522 through 1530 Processing helix chain 'K' and resid 1533 through 1537 Processing helix chain 'K' and resid 1543 through 1555 removed outlier: 3.833A pdb=" N ASN K1547 " --> pdb=" O ASP K1543 " (cutoff:3.500A) Processing helix chain 'K' and resid 1621 through 1628 Processing helix chain 'K' and resid 1663 through 1675 removed outlier: 4.352A pdb=" N PHE K1667 " --> pdb=" O GLY K1663 " (cutoff:3.500A) Processing helix chain 'K' and resid 1680 through 1698 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.745A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.015A 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: 7.738A 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: 6.498A 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: 7.393A 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 1226 through 1229 removed outlier: 3.740A pdb=" N LYS K1270 " --> pdb=" O TYR K1227 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER K1229 " --> pdb=" O GLU K1268 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU K1268 " --> pdb=" O SER K1229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1280 through 1282 Processing sheet with id=AB4, first strand: chain 'K' and resid 1357 through 1370 removed outlier: 6.825A pdb=" N ALA K1395 " --> pdb=" O VAL K1362 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER K1364 " --> pdb=" O THR K1393 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR K1393 " --> pdb=" O SER K1364 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP K1366 " --> pdb=" O TYR K1391 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR K1391 " --> pdb=" O ASP K1366 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR K1368 " --> pdb=" O PHE K1389 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE K1389 " --> pdb=" O THR K1368 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE K1410 " --> pdb=" O ALA K1398 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU K1400 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N CYS K1408 " --> pdb=" O GLU K1400 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE K1402 " --> pdb=" O ASP K1406 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP K1406 " --> pdb=" O ILE K1402 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR K1433 " --> pdb=" O HIS K1413 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN K1415 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE K1431 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR K1417 " --> pdb=" O VAL K1429 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL K1429 " --> pdb=" O TYR K1417 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TRP K1472 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TYR K1433 " --> pdb=" O TRP K1472 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 280 hydrogen bonds 560 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2780 1.33 - 1.45: 5676 1.45 - 1.57: 8411 1.57 - 1.69: 602 1.69 - 1.81: 68 Bond restraints: 17537 Sorted by residual: bond pdb=" NZ ALY B 16 " pdb=" CH ALY B 16 " ideal model delta sigma weight residual 1.343 1.384 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.71e+00 bond pdb=" CG GLU F 63 " pdb=" CD GLU F 63 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.62e+00 bond pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CD GLU F 63 " pdb=" OE1 GLU F 63 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.44e+00 ... (remaining 17532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 24357 1.84 - 3.67: 555 3.67 - 5.51: 45 5.51 - 7.34: 15 7.34 - 9.18: 3 Bond angle restraints: 24975 Sorted by residual: angle pdb=" C LEU H 101 " pdb=" N LEU H 102 " pdb=" CA LEU H 102 " ideal model delta sigma weight residual 122.70 113.52 9.18 1.98e+00 2.55e-01 2.15e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.28 117.11 -6.83 1.55e+00 4.16e-01 1.94e+01 angle pdb=" N GLU A 105 " pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " ideal model delta sigma weight residual 110.12 115.86 -5.74 1.47e+00 4.63e-01 1.52e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 118.05 -7.03 1.86e+00 2.89e-01 1.43e+01 angle pdb=" N GLU K1186 " pdb=" CA GLU K1186 " pdb=" CB GLU K1186 " ideal model delta sigma weight residual 110.12 115.43 -5.31 1.47e+00 4.63e-01 1.30e+01 ... (remaining 24970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 8491 35.55 - 71.11: 1338 71.11 - 106.66: 23 106.66 - 142.21: 1 142.21 - 177.77: 2 Dihedral angle restraints: 9855 sinusoidal: 6092 harmonic: 3763 Sorted by residual: dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 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 37.77 -177.77 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 61.88 158.12 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2205 0.039 - 0.079: 440 0.079 - 0.118: 109 0.118 - 0.157: 19 0.157 - 0.196: 1 Chirality restraints: 2774 Sorted by residual: chirality pdb=" CA GLU G 61 " pdb=" N GLU G 61 " pdb=" C GLU G 61 " pdb=" CB GLU G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA MET K1095 " pdb=" N MET K1095 " pdb=" C MET K1095 " pdb=" CB MET K1095 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" P DA J 60 " pdb=" OP1 DA J 60 " pdb=" OP2 DA J 60 " pdb=" O5' DA J 60 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2771 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO H 103 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ARG A 69 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 69 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 70 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO D 103 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.026 5.00e-02 4.00e+02 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1032 2.73 - 3.27: 15993 3.27 - 3.81: 32542 3.81 - 4.36: 37765 4.36 - 4.90: 55123 Nonbonded interactions: 142455 Sorted by model distance: nonbonded pdb=" O2 DT J 140 " pdb=" N6 DA J 141 " model vdw 2.187 3.120 nonbonded pdb=" OD2 ASP F 68 " pdb=" NE2 GLN F 93 " model vdw 2.223 3.120 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.224 3.120 nonbonded pdb=" O2 DT I 107 " pdb=" N2 DG J 75 " model vdw 2.237 3.120 nonbonded pdb=" N THR D 90 " pdb=" OE2 GLU D 93 " model vdw 2.258 3.120 ... (remaining 142450 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 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 124)) selection = (chain 'H' and resid 31 through 124) } ncs_group { reference = (chain 'I' and resid 16 through 165) selection = (chain 'J' and resid 16 through 165) } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.950 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 0.049 17537 Z= 0.173 Angle : 0.631 9.177 24975 Z= 0.383 Chirality : 0.035 0.196 2774 Planarity : 0.004 0.056 2132 Dihedral : 24.758 177.765 7427 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.26 (0.23), residues: 1261 helix: 1.26 (0.19), residues: 749 sheet: 0.06 (0.66), residues: 58 loop : 0.41 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K1502 HIS 0.003 0.001 HIS B 75 PHE 0.015 0.001 PHE A 104 TYR 0.019 0.001 TYR G 57 ARG 0.019 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7537 (mp0) cc_final: 0.7323 (mm-30) REVERT: E 110 CYS cc_start: 0.8206 (t) cc_final: 0.7997 (t) REVERT: E 120 MET cc_start: 0.7713 (ptp) cc_final: 0.7493 (mpp) REVERT: F 97 LEU cc_start: 0.8693 (tp) cc_final: 0.8338 (tp) REVERT: K 1148 GLN cc_start: 0.6269 (pp30) cc_final: 0.5746 (tp40) REVERT: K 1193 MET cc_start: -0.3248 (ttt) cc_final: -0.3778 (tpp) REVERT: K 1385 MET cc_start: -0.2374 (mtt) cc_final: -0.3087 (mpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2625 time to fit residues: 38.5689 Evaluate side-chains 54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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: 6.9990 chunk 117 optimal weight: 0.0010 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 F 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17537 Z= 0.196 Angle : 0.578 8.267 24975 Z= 0.336 Chirality : 0.036 0.177 2774 Planarity : 0.005 0.061 2132 Dihedral : 28.405 172.730 4825 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.49 (0.23), residues: 1261 helix: 1.43 (0.18), residues: 769 sheet: 0.31 (0.67), residues: 58 loop : 0.47 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K1502 HIS 0.007 0.001 HIS K1451 PHE 0.014 0.001 PHE A 67 TYR 0.012 0.001 TYR H 83 ARG 0.007 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9519 (mt) cc_final: 0.9289 (mt) REVERT: B 84 MET cc_start: 0.7541 (ppp) cc_final: 0.7239 (ppp) REVERT: F 58 LEU cc_start: 0.9469 (tp) cc_final: 0.9160 (pp) REVERT: F 97 LEU cc_start: 0.8766 (tp) cc_final: 0.8419 (tp) REVERT: K 1148 GLN cc_start: 0.6374 (pp30) cc_final: 0.6011 (tp40) REVERT: K 1193 MET cc_start: -0.2426 (ttt) cc_final: -0.3296 (tpp) REVERT: K 1691 MET cc_start: 0.6143 (ppp) cc_final: 0.5940 (ppp) outliers start: 2 outliers final: 2 residues processed: 80 average time/residue: 0.2544 time to fit residues: 33.9428 Evaluate side-chains 51 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 141 optimal weight: 40.0000 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 93 GLN F 93 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17537 Z= 0.233 Angle : 0.599 6.502 24975 Z= 0.349 Chirality : 0.036 0.153 2774 Planarity : 0.005 0.063 2132 Dihedral : 28.873 162.291 4825 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.18 % Allowed : 4.08 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.47 (0.23), residues: 1261 helix: 1.45 (0.18), residues: 775 sheet: 0.47 (0.65), residues: 62 loop : 0.33 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K1502 HIS 0.015 0.001 HIS D 109 PHE 0.014 0.001 PHE A 67 TYR 0.015 0.001 TYR H 83 ARG 0.019 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9547 (mt) cc_final: 0.9301 (mt) REVERT: C 87 ILE cc_start: 0.9182 (tp) cc_final: 0.8884 (pt) REVERT: F 97 LEU cc_start: 0.8875 (tp) cc_final: 0.8585 (tp) REVERT: K 1095 MET cc_start: 0.0573 (mmm) cc_final: 0.0223 (mmm) REVERT: K 1138 ILE cc_start: 0.7653 (tt) cc_final: 0.7416 (pt) outliers start: 2 outliers final: 0 residues processed: 77 average time/residue: 0.2449 time to fit residues: 31.7222 Evaluate side-chains 48 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 40.0000 chunk 149 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1638 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17537 Z= 0.218 Angle : 0.608 7.236 24975 Z= 0.353 Chirality : 0.037 0.201 2774 Planarity : 0.005 0.086 2132 Dihedral : 29.062 165.973 4825 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.37 (0.23), residues: 1261 helix: 1.39 (0.18), residues: 778 sheet: 0.55 (0.66), residues: 62 loop : 0.22 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1502 HIS 0.008 0.001 HIS K1451 PHE 0.022 0.001 PHE E 104 TYR 0.015 0.002 TYR B 72 ARG 0.012 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9547 (mt) cc_final: 0.9318 (mt) REVERT: A 105 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8414 (tm-30) REVERT: B 63 GLU cc_start: 0.8777 (mp0) cc_final: 0.8428 (mp0) REVERT: C 41 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7598 (mm-30) REVERT: K 1193 MET cc_start: -0.1627 (ttt) cc_final: -0.2612 (tpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2659 time to fit residues: 34.3959 Evaluate side-chains 51 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1628 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17537 Z= 0.280 Angle : 0.649 6.754 24975 Z= 0.377 Chirality : 0.038 0.186 2774 Planarity : 0.005 0.056 2132 Dihedral : 29.590 167.825 4825 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.19 (0.23), residues: 1261 helix: 1.27 (0.18), residues: 778 sheet: 0.46 (0.65), residues: 62 loop : 0.09 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K1502 HIS 0.005 0.001 HIS E 39 PHE 0.017 0.002 PHE E 104 TYR 0.017 0.002 TYR C 50 ARG 0.016 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9583 (mt) cc_final: 0.9360 (mt) REVERT: B 88 TYR cc_start: 0.8529 (m-10) cc_final: 0.8300 (m-10) REVERT: C 41 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 87 ILE cc_start: 0.9338 (tp) cc_final: 0.8997 (pt) REVERT: F 68 ASP cc_start: 0.8374 (m-30) cc_final: 0.8097 (m-30) REVERT: F 97 LEU cc_start: 0.8841 (tp) cc_final: 0.8616 (tp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2458 time to fit residues: 28.8711 Evaluate side-chains 48 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1336 ASN ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17537 Z= 0.266 Angle : 0.641 6.929 24975 Z= 0.372 Chirality : 0.038 0.175 2774 Planarity : 0.005 0.056 2132 Dihedral : 29.858 170.629 4825 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.10 (0.23), residues: 1261 helix: 1.22 (0.18), residues: 776 sheet: 0.25 (0.65), residues: 64 loop : 0.07 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K1502 HIS 0.005 0.001 HIS K1451 PHE 0.014 0.002 PHE A 67 TYR 0.016 0.002 TYR G 57 ARG 0.009 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9558 (mt) cc_final: 0.9336 (mt) REVERT: A 105 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 63 GLU cc_start: 0.8749 (mp0) cc_final: 0.8535 (mp0) REVERT: B 88 TYR cc_start: 0.8528 (m-10) cc_final: 0.8097 (m-10) REVERT: C 41 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 87 ILE cc_start: 0.9332 (tp) cc_final: 0.9032 (pt) REVERT: K 1193 MET cc_start: -0.0858 (ttt) cc_final: -0.1108 (ttm) REVERT: K 1506 MET cc_start: -0.2361 (mtt) cc_final: -0.2809 (tpp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2815 time to fit residues: 30.2507 Evaluate side-chains 46 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 55 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN K1113 GLN ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1547 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 17537 Z= 0.381 Angle : 0.759 7.948 24975 Z= 0.435 Chirality : 0.042 0.207 2774 Planarity : 0.006 0.053 2132 Dihedral : 30.600 170.410 4825 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.09 % Allowed : 1.72 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1261 helix: 0.74 (0.18), residues: 779 sheet: 0.26 (0.65), residues: 64 loop : -0.34 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K1472 HIS 0.007 0.002 HIS K1413 PHE 0.027 0.002 PHE G 25 TYR 0.017 0.002 TYR F 88 ARG 0.015 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9598 (mt) cc_final: 0.9381 (mt) REVERT: B 88 TYR cc_start: 0.8628 (m-10) cc_final: 0.8248 (m-10) REVERT: E 105 GLU cc_start: 0.8652 (pm20) cc_final: 0.8409 (pm20) REVERT: K 1193 MET cc_start: 0.0674 (ttt) cc_final: 0.0338 (ttm) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.2532 time to fit residues: 28.5020 Evaluate side-chains 48 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 135 optimal weight: 0.0070 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17537 Z= 0.188 Angle : 0.635 7.896 24975 Z= 0.365 Chirality : 0.037 0.171 2774 Planarity : 0.005 0.149 2132 Dihedral : 30.290 172.598 4825 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1261 helix: 1.21 (0.18), residues: 776 sheet: 0.22 (0.67), residues: 64 loop : -0.00 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K1472 HIS 0.007 0.001 HIS K1413 PHE 0.013 0.001 PHE A 67 TYR 0.012 0.001 TYR G 57 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9528 (mt) cc_final: 0.9316 (mt) REVERT: A 105 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8302 (tm-30) REVERT: B 63 GLU cc_start: 0.8847 (mp0) cc_final: 0.8559 (mp0) REVERT: B 88 TYR cc_start: 0.8532 (m-10) cc_final: 0.8130 (m-10) REVERT: E 105 GLU cc_start: 0.8735 (pm20) cc_final: 0.8524 (pm20) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2579 time to fit residues: 34.5710 Evaluate side-chains 53 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17537 Z= 0.278 Angle : 0.666 10.517 24975 Z= 0.382 Chirality : 0.038 0.153 2774 Planarity : 0.005 0.123 2132 Dihedral : 30.361 169.387 4825 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1261 helix: 1.14 (0.18), residues: 776 sheet: 0.33 (0.69), residues: 64 loop : -0.14 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K1472 HIS 0.005 0.002 HIS B 75 PHE 0.026 0.002 PHE G 25 TYR 0.010 0.002 TYR B 72 ARG 0.007 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9542 (mt) cc_final: 0.9318 (mt) REVERT: A 105 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8305 (tm-30) REVERT: B 63 GLU cc_start: 0.8853 (mp0) cc_final: 0.8578 (mp0) REVERT: B 88 TYR cc_start: 0.8567 (m-10) cc_final: 0.8196 (m-10) REVERT: K 1158 TRP cc_start: 0.8795 (m100) cc_final: 0.8558 (m100) REVERT: K 1193 MET cc_start: -0.0034 (ttt) cc_final: -0.0475 (ttm) REVERT: K 1506 MET cc_start: -0.1606 (mtt) cc_final: -0.2021 (tpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2814 time to fit residues: 33.0437 Evaluate side-chains 49 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 17537 Z= 0.374 Angle : 0.765 12.171 24975 Z= 0.434 Chirality : 0.042 0.186 2774 Planarity : 0.006 0.133 2132 Dihedral : 30.903 172.742 4825 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1261 helix: 0.54 (0.18), residues: 780 sheet: -0.01 (0.66), residues: 64 loop : -0.44 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K1158 HIS 0.008 0.002 HIS K1413 PHE 0.033 0.002 PHE G 25 TYR 0.014 0.002 TYR K1503 ARG 0.032 0.001 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9595 (mt) cc_final: 0.9381 (mt) REVERT: A 105 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8281 (tm-30) REVERT: B 63 GLU cc_start: 0.8916 (mp0) cc_final: 0.8658 (mp0) REVERT: B 88 TYR cc_start: 0.8684 (m-10) cc_final: 0.8299 (m-80) REVERT: C 87 ILE cc_start: 0.9343 (tp) cc_final: 0.9127 (pt) REVERT: E 105 GLU cc_start: 0.8758 (pm20) cc_final: 0.8556 (pm20) REVERT: K 1203 LYS cc_start: 0.4528 (tptt) cc_final: 0.3502 (ttmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2585 time to fit residues: 28.1979 Evaluate side-chains 47 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 0.0270 chunk 126 optimal weight: 8.9990 chunk 15 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.048097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.033233 restraints weight = 211477.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.034136 restraints weight = 108970.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.034540 restraints weight = 72361.532| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17537 Z= 0.192 Angle : 0.652 9.397 24975 Z= 0.373 Chirality : 0.038 0.169 2774 Planarity : 0.005 0.096 2132 Dihedral : 30.456 173.539 4825 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1261 helix: 1.05 (0.18), residues: 784 sheet: 0.16 (0.67), residues: 63 loop : -0.15 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K1472 HIS 0.007 0.001 HIS B 75 PHE 0.021 0.001 PHE G 25 TYR 0.015 0.001 TYR K1298 ARG 0.016 0.001 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.78 seconds wall clock time: 43 minutes 27.39 seconds (2607.39 seconds total)