Starting phenix.real_space_refine on Fri Jul 3 22:04:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_34595.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_34595.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_34595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_34595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_34595.map" model { file = "/net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_34595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hal_34595/07_2026/8hal_34595.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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-1': 1, 'ALY:plan-2': 2} 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: {'ASP:plan': 1, 'ARG:plan': 2} 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: {'ARG:plan': 2, 'GLU:plan': 1} 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: 3.24, per 1000 atoms: 0.20 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: 1.01 Conformation dependent library (CDL) restraints added in 620.4 milliseconds 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: 2.27 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: 3.79 Time building geometry restraints manager: 1.36 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=" C3' DA I 18 " pdb=" C2' DA I 18 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT J 107 " pdb=" C2' DT J 107 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT I 108 " pdb=" C2' DT I 108 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J 135 " pdb=" C2' DT J 135 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT J 145 " pdb=" C2' DT J 145 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 ... (remaining 17532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 23852 1.84 - 3.67: 1056 3.67 - 5.51: 49 5.51 - 7.34: 15 7.34 - 9.18: 3 Bond angle restraints: 24975 Sorted by residual: angle pdb=" O4' DT I 107 " pdb=" C4' DT I 107 " pdb=" C3' DT I 107 " ideal model delta sigma weight residual 106.00 102.71 3.29 6.00e-01 2.78e+00 3.00e+01 angle pdb=" O4' DC I 105 " pdb=" C4' DC I 105 " pdb=" C3' DC I 105 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.26e+01 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=" N3 DT I 65 " pdb=" C4 DT I 65 " pdb=" O4 DT I 65 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+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 ... (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: 1818 0.039 - 0.079: 694 0.079 - 0.118: 238 0.118 - 0.157: 22 0.157 - 0.196: 2 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=" C3' DT I 136 " pdb=" C4' DT I 136 " pdb=" O3' DT I 136 " pdb=" C2' DT I 136 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.26e-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 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.77e-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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.280 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17537 Z= 0.454 Angle : 0.758 9.177 24975 Z= 0.633 Chirality : 0.044 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 : 12.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.019 0.001 ARG E 63 TYR 0.019 0.001 TYR G 57 PHE 0.015 0.001 PHE A 104 TRP 0.024 0.001 TRP K1502 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.45 (17537) covalent geometry : angle 0.75807 / 0.63 (24975) hydrogen bonds : bond 0.13883 / 8.98 ( 863) hydrogen bonds : angle 5.77810 / 4.15 ( 2285) *********************** 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 : 0.498 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: 0.7998 (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: 0.1138 time to fit residues: 16.9983 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 : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS E 93 GLN F 93 GLN G 38 ASN G 104 GLN H 109 HIS K1628 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.052874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.037422 restraints weight = 209299.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038384 restraints weight = 110804.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.038815 restraints weight = 75470.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.039275 restraints weight = 60687.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.039400 restraints weight = 53288.096| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 17537 Z= 0.296 Angle : 0.845 11.124 24975 Z= 0.468 Chirality : 0.048 0.356 2774 Planarity : 0.007 0.075 2132 Dihedral : 29.262 163.458 4825 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.54 % Allowed : 5.08 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.22), residues: 1261 helix: 0.64 (0.18), residues: 773 sheet: 0.38 (0.64), residues: 62 loop : 0.22 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.022 0.003 TYR H 83 PHE 0.024 0.003 PHE H 70 TRP 0.054 0.005 TRP K1502 HIS 0.016 0.003 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.30 (17537) covalent geometry : angle 0.84453 / 0.47 (24975) hydrogen bonds : bond 0.10499 / 7.05 ( 863) hydrogen bonds : angle 4.64993 / 3.33 ( 2285) *********************** 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 76 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9535 (mt) cc_final: 0.9326 (mt) REVERT: B 59 LYS cc_start: 0.9121 (ttpp) cc_final: 0.8873 (ttpp) REVERT: D 62 MET cc_start: 0.8728 (tpp) cc_final: 0.8462 (tpp) REVERT: F 58 LEU cc_start: 0.9515 (tp) cc_final: 0.9126 (pp) REVERT: F 63 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: F 97 LEU cc_start: 0.8807 (tp) cc_final: 0.8513 (tp) REVERT: K 1095 MET cc_start: 0.1340 (mmm) cc_final: 0.1027 (mmm) REVERT: K 1193 MET cc_start: 0.0651 (ttt) cc_final: -0.0714 (tpp) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.1025 time to fit residues: 13.0247 Evaluate side-chains 50 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 129 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 109 HIS F 93 GLN G 104 GLN K1547 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.051072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.035755 restraints weight = 211181.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.036697 restraints weight = 109805.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.037261 restraints weight = 73345.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.037491 restraints weight = 58303.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.037726 restraints weight = 52323.818| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17537 Z= 0.246 Angle : 0.728 9.923 24975 Z= 0.420 Chirality : 0.045 0.336 2774 Planarity : 0.006 0.058 2132 Dihedral : 29.686 167.228 4825 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1261 helix: 0.66 (0.17), residues: 772 sheet: 0.30 (0.65), residues: 64 loop : -0.04 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 69 TYR 0.024 0.002 TYR B 51 PHE 0.028 0.002 PHE K1206 TRP 0.012 0.002 TRP K1502 HIS 0.007 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.25 (17537) covalent geometry : angle 0.72797 / 0.42 (24975) hydrogen bonds : bond 0.07081 / 4.81 ( 863) hydrogen bonds : angle 4.48944 / 3.17 ( 2285) *********************** 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 75 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9555 (mt) cc_final: 0.9333 (mt) REVERT: B 84 MET cc_start: 0.7498 (ppp) cc_final: 0.7234 (ppp) REVERT: B 88 TYR cc_start: 0.8581 (m-10) cc_final: 0.8190 (m-10) REVERT: D 62 MET cc_start: 0.8757 (tpp) cc_final: 0.8459 (tpp) REVERT: D 105 GLU cc_start: 0.8410 (tp30) cc_final: 0.8179 (tp30) REVERT: F 68 ASP cc_start: 0.8450 (m-30) cc_final: 0.8162 (m-30) REVERT: F 97 LEU cc_start: 0.8935 (tp) cc_final: 0.8660 (tp) outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.1113 time to fit residues: 13.7550 Evaluate side-chains 48 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 150 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 40.0000 chunk 102 optimal weight: 30.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.051280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.035851 restraints weight = 210721.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.036810 restraints weight = 108916.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.037236 restraints weight = 72570.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.037663 restraints weight = 58409.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037791 restraints weight = 51545.271| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3454 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= 0.168 Angle : 0.646 6.706 24975 Z= 0.376 Chirality : 0.042 0.310 2774 Planarity : 0.004 0.058 2132 Dihedral : 29.636 170.620 4825 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1261 helix: 1.04 (0.18), residues: 770 sheet: 0.53 (0.66), residues: 64 loop : -0.07 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 52 TYR 0.011 0.002 TYR B 51 PHE 0.021 0.002 PHE G 25 TRP 0.020 0.002 TRP K1158 HIS 0.007 0.001 HIS K1451 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (17537) covalent geometry : angle 0.64617 / 0.38 (24975) hydrogen bonds : bond 0.06188 / 4.13 ( 863) hydrogen bonds : angle 4.14807 / 2.91 ( 2285) *********************** 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 73 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9532 (mt) cc_final: 0.9303 (mt) REVERT: B 84 MET cc_start: 0.7754 (ppp) cc_final: 0.7519 (ppp) REVERT: B 88 TYR cc_start: 0.8581 (m-10) cc_final: 0.8128 (m-10) REVERT: C 87 ILE cc_start: 0.9248 (tp) cc_final: 0.8856 (pt) REVERT: D 62 MET cc_start: 0.8815 (tpp) cc_final: 0.8490 (tpp) REVERT: F 97 LEU cc_start: 0.8997 (tp) cc_final: 0.8738 (tp) REVERT: K 1193 MET cc_start: 0.0992 (ttt) cc_final: -0.0519 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1090 time to fit residues: 13.5254 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 84 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN K1638 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.051261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.035936 restraints weight = 209181.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.036902 restraints weight = 108576.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.037443 restraints weight = 71906.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037744 restraints weight = 57101.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.037809 restraints weight = 50688.475| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17537 Z= 0.153 Angle : 0.632 6.614 24975 Z= 0.366 Chirality : 0.041 0.319 2774 Planarity : 0.005 0.106 2132 Dihedral : 29.646 171.030 4825 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1261 helix: 1.20 (0.18), residues: 771 sheet: 0.44 (0.66), residues: 64 loop : -0.11 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.009 0.001 TYR B 88 PHE 0.017 0.001 PHE A 67 TRP 0.011 0.001 TRP K1502 HIS 0.016 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (17537) covalent geometry : angle 0.63247 / 0.37 (24975) hydrogen bonds : bond 0.05644 / 3.76 ( 863) hydrogen bonds : angle 4.02877 / 2.82 ( 2285) *********************** 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 73 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9506 (mt) cc_final: 0.9271 (mt) REVERT: A 105 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8411 (tm-30) REVERT: B 84 MET cc_start: 0.8086 (ppp) cc_final: 0.7805 (ppp) REVERT: B 88 TYR cc_start: 0.8576 (m-10) cc_final: 0.8053 (m-10) REVERT: C 87 ILE cc_start: 0.9302 (tp) cc_final: 0.8953 (pt) REVERT: D 62 MET cc_start: 0.8832 (tpp) cc_final: 0.8507 (tpp) REVERT: F 97 LEU cc_start: 0.9074 (tp) cc_final: 0.8819 (tp) REVERT: K 1193 MET cc_start: 0.0863 (ttt) cc_final: -0.0882 (tpp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1067 time to fit residues: 13.1734 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 24 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 114 optimal weight: 0.5980 chunk 85 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.050358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.035273 restraints weight = 211557.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036211 restraints weight = 110095.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.036745 restraints weight = 73241.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.036948 restraints weight = 57986.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.037178 restraints weight = 52254.309| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17537 Z= 0.173 Angle : 0.649 8.078 24975 Z= 0.376 Chirality : 0.042 0.317 2774 Planarity : 0.005 0.063 2132 Dihedral : 29.734 172.227 4825 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1261 helix: 1.17 (0.18), residues: 777 sheet: 0.31 (0.65), residues: 64 loop : -0.13 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 52 TYR 0.010 0.001 TYR C 39 PHE 0.015 0.001 PHE A 67 TRP 0.008 0.001 TRP K1502 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (17537) covalent geometry : angle 0.64921 / 0.38 (24975) hydrogen bonds : bond 0.06207 / 4.17 ( 863) hydrogen bonds : angle 4.07294 / 2.85 ( 2285) *********************** 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 68 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9528 (mt) cc_final: 0.9297 (mt) REVERT: A 105 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 84 MET cc_start: 0.7955 (ppp) cc_final: 0.7694 (ppp) REVERT: B 88 TYR cc_start: 0.8661 (m-10) cc_final: 0.8237 (m-10) REVERT: C 87 ILE cc_start: 0.9294 (tp) cc_final: 0.8985 (pt) REVERT: D 62 MET cc_start: 0.8825 (tpp) cc_final: 0.8497 (tpp) REVERT: E 105 GLU cc_start: 0.8615 (pm20) cc_final: 0.8300 (pm20) REVERT: K 1193 MET cc_start: 0.0869 (ttt) cc_final: -0.1055 (tpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1093 time to fit residues: 12.7641 Evaluate side-chains 45 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 13 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.050851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.035668 restraints weight = 209894.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.036652 restraints weight = 108574.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.037080 restraints weight = 71751.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.037509 restraints weight = 57574.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.037619 restraints weight = 50585.584| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17537 Z= 0.139 Angle : 0.625 8.511 24975 Z= 0.362 Chirality : 0.041 0.322 2774 Planarity : 0.004 0.059 2132 Dihedral : 29.687 172.276 4825 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1261 helix: 1.27 (0.18), residues: 777 sheet: 0.33 (0.64), residues: 64 loop : -0.03 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.010 0.001 TYR B 72 PHE 0.017 0.001 PHE A 67 TRP 0.025 0.002 TRP K1472 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (17537) covalent geometry : angle 0.62486 / 0.36 (24975) hydrogen bonds : bond 0.05194 / 3.44 ( 863) hydrogen bonds : angle 3.98151 / 2.78 ( 2285) *********************** 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 71 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9511 (mt) cc_final: 0.9280 (mt) REVERT: A 105 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8356 (tm-30) REVERT: B 84 MET cc_start: 0.8014 (ppp) cc_final: 0.7799 (ppp) REVERT: B 88 TYR cc_start: 0.8645 (m-10) cc_final: 0.8245 (m-10) REVERT: C 87 ILE cc_start: 0.9241 (tp) cc_final: 0.8965 (pt) REVERT: D 62 MET cc_start: 0.8819 (tpp) cc_final: 0.8462 (tpp) REVERT: F 68 ASP cc_start: 0.8490 (m-30) cc_final: 0.8280 (m-30) REVERT: H 93 GLU cc_start: 0.8597 (mp0) cc_final: 0.8289 (mp0) REVERT: K 1193 MET cc_start: 0.1041 (ttt) cc_final: -0.0954 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1061 time to fit residues: 12.9872 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 : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 108 optimal weight: 0.3980 chunk 123 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 50.0000 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** 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 = 0.3507 r_free = 0.3507 target = 0.050878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.035646 restraints weight = 210880.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.036615 restraints weight = 108842.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.037179 restraints weight = 71488.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.037434 restraints weight = 56513.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.037496 restraints weight = 50343.751| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17537 Z= 0.137 Angle : 0.626 7.854 24975 Z= 0.363 Chirality : 0.041 0.314 2774 Planarity : 0.004 0.059 2132 Dihedral : 29.639 172.542 4825 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.23), residues: 1261 helix: 1.26 (0.18), residues: 777 sheet: 0.25 (0.65), residues: 64 loop : -0.00 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 52 TYR 0.011 0.001 TYR G 57 PHE 0.016 0.001 PHE A 67 TRP 0.014 0.001 TRP K1472 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (17537) covalent geometry : angle 0.62590 / 0.36 (24975) hydrogen bonds : bond 0.05120 / 3.39 ( 863) hydrogen bonds : angle 3.96180 / 2.75 ( 2285) *********************** 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 71 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9506 (mt) cc_final: 0.9274 (mt) REVERT: A 105 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 63 GLU cc_start: 0.8886 (mp0) cc_final: 0.8650 (mp0) REVERT: B 84 MET cc_start: 0.8039 (ppp) cc_final: 0.7822 (ppp) REVERT: B 88 TYR cc_start: 0.8637 (m-10) cc_final: 0.8238 (m-10) REVERT: C 87 ILE cc_start: 0.9249 (tp) cc_final: 0.8969 (pt) REVERT: D 62 MET cc_start: 0.8836 (tpp) cc_final: 0.8467 (tpp) REVERT: F 68 ASP cc_start: 0.8500 (m-30) cc_final: 0.8293 (m-30) REVERT: F 97 LEU cc_start: 0.9018 (tp) cc_final: 0.8718 (tp) REVERT: H 93 GLU cc_start: 0.8551 (mp0) cc_final: 0.8211 (mp0) REVERT: K 1193 MET cc_start: 0.0939 (ttt) cc_final: -0.1025 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1083 time to fit residues: 12.6908 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 : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 144 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 147 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** 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 = 0.3493 r_free = 0.3493 target = 0.050297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.035194 restraints weight = 212257.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.036158 restraints weight = 109413.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.036584 restraints weight = 72731.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.036969 restraints weight = 58338.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.037106 restraints weight = 51410.680| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17537 Z= 0.155 Angle : 0.635 6.804 24975 Z= 0.366 Chirality : 0.041 0.313 2774 Planarity : 0.004 0.059 2132 Dihedral : 29.690 172.799 4825 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.23), residues: 1261 helix: 1.32 (0.18), residues: 775 sheet: 0.28 (0.65), residues: 64 loop : -0.03 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 52 TYR 0.012 0.001 TYR G 57 PHE 0.015 0.001 PHE A 67 TRP 0.015 0.002 TRP K1151 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (17537) covalent geometry : angle 0.63521 / 0.37 (24975) hydrogen bonds : bond 0.05603 / 3.75 ( 863) hydrogen bonds : angle 3.99448 / 2.78 ( 2285) *********************** 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 73 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9535 (mt) cc_final: 0.9313 (mt) REVERT: A 105 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 63 GLU cc_start: 0.8867 (mp0) cc_final: 0.8597 (mp0) REVERT: B 84 MET cc_start: 0.8056 (ppp) cc_final: 0.7823 (ppp) REVERT: B 88 TYR cc_start: 0.8551 (m-10) cc_final: 0.8280 (m-10) REVERT: C 87 ILE cc_start: 0.9277 (tp) cc_final: 0.8983 (pt) REVERT: D 62 MET cc_start: 0.8856 (tpp) cc_final: 0.8499 (tpp) REVERT: H 93 GLU cc_start: 0.8654 (mp0) cc_final: 0.8312 (mp0) REVERT: H 105 GLU cc_start: 0.8451 (pm20) cc_final: 0.8232 (pm20) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1188 time to fit residues: 14.3159 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 : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 90 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 88 optimal weight: 50.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1351 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 = 0.3475 r_free = 0.3475 target = 0.049605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.034475 restraints weight = 212923.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035426 restraints weight = 109802.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.035981 restraints weight = 72400.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.036291 restraints weight = 57016.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.036374 restraints weight = 50159.257| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17537 Z= 0.177 Angle : 0.669 6.969 24975 Z= 0.384 Chirality : 0.042 0.321 2774 Planarity : 0.005 0.059 2132 Dihedral : 29.853 173.868 4825 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.23), residues: 1261 helix: 1.17 (0.18), residues: 775 sheet: 0.45 (0.65), residues: 64 loop : -0.12 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 52 TYR 0.014 0.001 TYR G 57 PHE 0.016 0.001 PHE A 67 TRP 0.023 0.002 TRP K1158 HIS 0.021 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (17537) covalent geometry : angle 0.66915 / 0.38 (24975) hydrogen bonds : bond 0.06325 / 4.25 ( 863) hydrogen bonds : angle 4.17843 / 2.91 ( 2285) ********************** 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 73 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.9539 (mt) cc_final: 0.9315 (mt) REVERT: A 105 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 88 TYR cc_start: 0.8530 (m-10) cc_final: 0.8175 (m-10) REVERT: C 87 ILE cc_start: 0.9314 (tp) cc_final: 0.9079 (pt) REVERT: D 62 MET cc_start: 0.8813 (tpp) cc_final: 0.8399 (tpp) REVERT: H 93 GLU cc_start: 0.8646 (mp0) cc_final: 0.8305 (mp0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1050 time to fit residues: 12.6300 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 : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 7.9990 chunk 89 optimal weight: 40.0000 chunk 145 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 50.0000 chunk 150 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN ** K1351 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 = 0.3433 r_free = 0.3433 target = 0.047921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.032965 restraints weight = 218046.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.033829 restraints weight = 115394.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.034348 restraints weight = 77840.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.034566 restraints weight = 62225.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.034759 restraints weight = 55684.759| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5409 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= 0.234 Angle : 0.778 9.384 24975 Z= 0.435 Chirality : 0.045 0.340 2774 Planarity : 0.006 0.059 2132 Dihedral : 30.343 176.872 4825 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1261 helix: 0.83 (0.18), residues: 774 sheet: 0.10 (0.63), residues: 64 loop : -0.42 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 42 TYR 0.021 0.002 TYR H 40 PHE 0.019 0.002 PHE E 78 TRP 0.013 0.002 TRP K1545 HIS 0.009 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (17537) covalent geometry : angle 0.77751 / 0.44 (24975) hydrogen bonds : bond 0.08631 / 5.90 ( 863) hydrogen bonds : angle 4.54982 / 3.19 ( 2285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.25 seconds wall clock time: 55 minutes 10.03 seconds (3310.03 seconds total)