Starting phenix.real_space_refine on Thu Aug 6 20:16:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8haj_34592/08_2026/8haj_34592.cif" } resolution = 4.8 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 326 5.49 5 S 47 5.16 5 C 9860 2.51 5 N 3138 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17214 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: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'ALY:plan-2': 2} Unresolved non-hydrogen planarities: 2 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: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3362 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 3320 Classifications: {'DNA': 162} Link IDs: {'rna3p': 161} Chain: "K" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4403 Classifications: {'peptide': 533} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 499} Chain breaks: 3 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: 3.70, per 1000 atoms: 0.21 Number of scatterers: 17214 At special positions: 0 Unit cell: (107.31, 163.17, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 326 15.00 O 3843 8.00 N 3138 7.00 C 9860 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: 1.56 Conformation dependent library (CDL) restraints added in 395.6 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 60.7% alpha, 6.5% beta 115 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.669A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.794A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.016A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.581A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) 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: 4.507A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.542A 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.586A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.883A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.810A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.367A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.552A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 1051 through 1068 removed outlier: 4.161A pdb=" N GLN K1056 " --> pdb=" O GLU K1052 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA K1057 " --> pdb=" O GLU K1053 " (cutoff:3.500A) Proline residue: K1060 - end of helix Processing helix chain 'K' and resid 1072 through 1077 removed outlier: 4.399A pdb=" N GLN K1077 " --> pdb=" O LEU K1073 " (cutoff:3.500A) Processing helix chain 'K' and resid 1088 through 1093 Processing helix chain 'K' and resid 1098 through 1109 Processing helix chain 'K' and resid 1113 through 1132 removed outlier: 3.775A pdb=" N TYR K1117 " --> pdb=" O GLU K1113 " (cutoff:3.500A) Processing helix chain 'K' and resid 1136 through 1159 removed outlier: 3.596A pdb=" N GLU K1152 " --> pdb=" O VAL K1148 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP K1154 " --> pdb=" O GLU K1150 " (cutoff:3.500A) Proline residue: K1155 - end of helix Processing helix chain 'K' and resid 1201 through 1208 removed outlier: 3.584A pdb=" N PHE K1205 " --> pdb=" O CYS K1201 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN K1206 " --> pdb=" O GLU K1202 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU K1207 " --> pdb=" O LYS K1203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K1208 " --> pdb=" O CYS K1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1201 through 1208' Processing helix chain 'K' and resid 1272 through 1279 Processing helix chain 'K' and resid 1296 through 1314 Processing helix chain 'K' and resid 1336 through 1343 Processing helix chain 'K' and resid 1406 through 1429 removed outlier: 4.100A pdb=" N THR K1411 " --> pdb=" O LYS K1407 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA K1412 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K1427 " --> pdb=" O GLU K1423 " (cutoff:3.500A) Processing helix chain 'K' and resid 1459 through 1477 Processing helix chain 'K' and resid 1486 through 1493 Processing helix chain 'K' and resid 1497 through 1501 Processing helix chain 'K' and resid 1507 through 1519 removed outlier: 3.881A pdb=" N ASN K1511 " --> pdb=" O ASP K1507 " (cutoff:3.500A) Processing helix chain 'K' and resid 1579 through 1591 Processing helix chain 'K' and resid 1626 through 1638 removed outlier: 3.915A pdb=" N PHE K1630 " --> pdb=" O GLY K1626 " (cutoff:3.500A) Processing helix chain 'K' and resid 1643 through 1664 removed outlier: 4.048A pdb=" N GLN K1663 " --> pdb=" O HIS K1659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.161A 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: 7.018A 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: 7.062A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.950A 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: 7.239A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 1175 through 1176 removed outlier: 4.151A pdb=" N LEU K1175 " --> pdb=" O ILE K1185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1192 through 1194 Processing sheet with id=AB4, first strand: chain 'K' and resid 1244 through 1246 Processing sheet with id=AB5, first strand: chain 'K' and resid 1321 through 1334 removed outlier: 6.893A pdb=" N ALA K1359 " --> pdb=" O VAL K1326 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA K1328 " --> pdb=" O THR K1357 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR K1357 " --> pdb=" O ALA K1328 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP K1330 " --> pdb=" O TYR K1355 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR K1355 " --> pdb=" O ASP K1330 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR K1332 " --> pdb=" O PHE K1353 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE K1353 " --> pdb=" O THR K1332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE K1374 " --> pdb=" O ALA K1362 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU K1364 " --> pdb=" O CYS K1372 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N CYS K1372 " --> pdb=" O GLU K1364 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE K1366 " --> pdb=" O ASP K1370 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASP K1370 " --> pdb=" O ILE K1366 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N HIS K1377 " --> pdb=" O SER K1396 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP K1436 " --> pdb=" O ILE K1395 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR K1397 " --> pdb=" O TRP K1436 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 548 hydrogen bond angles 0 basepair planarities 115 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 4.55 Time building geometry restraints manager: 2.01 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: 3161 1.33 - 1.45: 5678 1.45 - 1.57: 8664 1.57 - 1.69: 650 1.69 - 1.81: 70 Bond restraints: 18223 Sorted by residual: bond pdb=" C3' DT I 108 " pdb=" C2' DT I 108 " 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 135 " pdb=" C2' DT J 135 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DA I 18 " pdb=" C2' DA I 18 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA I 41 " pdb=" C2' DA I 41 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DG I 111 " pdb=" C2' DG I 111 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.92e+00 ... (remaining 18218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 24764 1.73 - 3.46: 1164 3.46 - 5.20: 58 5.20 - 6.93: 15 6.93 - 8.66: 4 Bond angle restraints: 26005 Sorted by residual: angle pdb=" O4' DC J 106 " pdb=" C4' DC J 106 " pdb=" C3' DC J 106 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" N3 DT J 153 " pdb=" C4 DT J 153 " pdb=" O4 DT J 153 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 40 " pdb=" C4 DT I 40 " pdb=" O4 DT I 40 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 65 " pdb=" C4 DT I 65 " pdb=" O4 DT I 65 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 109 " pdb=" C4 DT J 109 " pdb=" O4 DT J 109 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 26000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.76: 8594 32.76 - 65.53: 1586 65.53 - 98.29: 38 98.29 - 131.05: 0 131.05 - 163.82: 2 Dihedral angle restraints: 10220 sinusoidal: 6415 harmonic: 3805 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+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 220.00 56.18 163.82 1 3.50e+01 8.16e-04 1.54e+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 66.76 153.24 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 10217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1537 0.030 - 0.060: 883 0.060 - 0.091: 341 0.091 - 0.121: 118 0.121 - 0.151: 14 Chirality restraints: 2893 Sorted by residual: chirality pdb=" CA PRO E 121 " pdb=" N PRO E 121 " pdb=" C PRO E 121 " pdb=" CB PRO E 121 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-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 -2.48 -0.14 2.00e-01 2.50e+01 5.05e-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 -2.60 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2890 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K1336 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO K1337 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO K1337 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K1337 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO H 100 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET K1059 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO K1060 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO K1060 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K1060 " 0.026 5.00e-02 4.00e+02 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1764 2.75 - 3.29: 16508 3.29 - 3.83: 33626 3.83 - 4.36: 38112 4.36 - 4.90: 55970 Nonbonded interactions: 145980 Sorted by model distance: nonbonded pdb=" OE1 GLN K1379 " pdb=" OG SER K1396 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR G 50 " pdb=" OE1 GLN H 92 " model vdw 2.230 3.040 nonbonded pdb=" O THR K1496 " pdb=" OG SER K1581 " model vdw 2.231 3.040 nonbonded pdb=" O GLU F 74 " pdb=" NH2 ARG H 89 " model vdw 2.277 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.282 3.040 ... (remaining 145975 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 28 and (name N or name CA or name C or name O or name CB \ )) or resid 29 through 121)) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 10 through 169) selection = (chain 'J' and resid 10 through 169) } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 0.041 18223 Z= 0.455 Angle : 0.744 8.661 26005 Z= 0.631 Chirality : 0.043 0.151 2893 Planarity : 0.004 0.061 2182 Dihedral : 24.856 163.816 7764 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.21 (0.23), residues: 1276 helix: 1.37 (0.19), residues: 761 sheet: 0.14 (0.61), residues: 65 loop : 0.06 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 69 TYR 0.011 0.001 TYR K1117 PHE 0.020 0.001 PHE K1508 TRP 0.011 0.001 TRP K1466 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.45 (18223) covalent geometry : angle 0.74390 / 0.63 (26005) hydrogen bonds : bond 0.14477 / 9.90 ( 865) hydrogen bonds : angle 5.51504 / 3.95 ( 2279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9156 (tp30) cc_final: 0.8689 (tt0) REVERT: D 34 TYR cc_start: 0.9157 (m-10) cc_final: 0.8885 (m-80) REVERT: G 78 ILE cc_start: 0.9124 (mt) cc_final: 0.8806 (mm) REVERT: K 1129 TRP cc_start: 0.7371 (m-10) cc_final: 0.7169 (m-10) REVERT: K 1478 ARG cc_start: 0.4409 (mmp-170) cc_final: 0.3607 (tpm170) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1190 time to fit residues: 18.2408 Evaluate side-chains 63 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 overall best weight: 3.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 108 ASN F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1056 GLN K1132 ASN K1236 ASN ** K1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1661 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.040925 restraints weight = 219242.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.041920 restraints weight = 125003.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.042341 restraints weight = 83247.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.042873 restraints weight = 65068.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.043028 restraints weight = 56720.237| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18223 Z= 0.182 Angle : 0.625 7.209 26005 Z= 0.365 Chirality : 0.040 0.325 2893 Planarity : 0.005 0.059 2182 Dihedral : 28.588 168.571 5103 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.44 % Allowed : 2.13 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.66 (0.23), residues: 1276 helix: 1.78 (0.18), residues: 774 sheet: 0.08 (0.61), residues: 66 loop : 0.15 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K1055 TYR 0.012 0.001 TYR F 72 PHE 0.018 0.002 PHE K1508 TRP 0.012 0.001 TRP K1466 HIS 0.012 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.18 (18223) covalent geometry : angle 0.62497 / 0.37 (26005) hydrogen bonds : bond 0.07237 / 4.97 ( 865) hydrogen bonds : angle 3.80285 / 2.75 ( 2279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9484 (tp30) cc_final: 0.9195 (tt0) REVERT: A 106 ASP cc_start: 0.8979 (t0) cc_final: 0.8618 (m-30) REVERT: E 67 PHE cc_start: 0.8923 (t80) cc_final: 0.8383 (t80) REVERT: E 92 LEU cc_start: 0.9447 (mp) cc_final: 0.9205 (tt) REVERT: G 78 ILE cc_start: 0.9084 (mt) cc_final: 0.8870 (mm) REVERT: H 99 LEU cc_start: 0.8093 (tp) cc_final: 0.7799 (tp) REVERT: K 1157 MET cc_start: 0.3336 (ttp) cc_final: 0.2516 (ttt) REVERT: K 1254 MET cc_start: 0.0971 (tpt) cc_final: -0.1044 (ptt) REVERT: K 1478 ARG cc_start: 0.5607 (mmp-170) cc_final: 0.5000 (tpm170) outliers start: 5 outliers final: 4 residues processed: 83 average time/residue: 0.1125 time to fit residues: 15.6679 Evaluate side-chains 64 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 78 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 108 ASN F 93 GLN H 92 GLN K1236 ASN K1638 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.050974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.032635 restraints weight = 225291.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.033792 restraints weight = 124518.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.034538 restraints weight = 83650.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.034908 restraints weight = 63960.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.035240 restraints weight = 54161.865| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18223 Z= 0.266 Angle : 0.749 9.476 26005 Z= 0.432 Chirality : 0.043 0.321 2893 Planarity : 0.007 0.060 2182 Dihedral : 29.288 177.031 5103 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.27 % Allowed : 4.17 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.40 (0.23), residues: 1276 helix: 1.47 (0.18), residues: 773 sheet: 0.33 (0.71), residues: 55 loop : 0.21 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 40 TYR 0.037 0.003 TYR K1355 PHE 0.021 0.003 PHE K1508 TRP 0.015 0.002 TRP K1466 HIS 0.010 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.27 (18223) covalent geometry : angle 0.74934 / 0.43 (26005) hydrogen bonds : bond 0.10236 / 7.08 ( 865) hydrogen bonds : angle 4.08061 / 2.95 ( 2279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9102 (t0) cc_final: 0.8899 (m-30) REVERT: E 41 TYR cc_start: 0.8482 (m-80) cc_final: 0.7998 (m-80) REVERT: K 1478 ARG cc_start: 0.5515 (mmp-170) cc_final: 0.4929 (tpm170) outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.1232 time to fit residues: 15.2195 Evaluate side-chains 52 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN K1261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.055505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037353 restraints weight = 227542.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.038356 restraints weight = 127710.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038767 restraints weight = 83310.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.039186 restraints weight = 65711.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.039240 restraints weight = 56650.794| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 18223 Z= 0.142 Angle : 0.611 11.733 26005 Z= 0.354 Chirality : 0.041 0.372 2893 Planarity : 0.005 0.059 2182 Dihedral : 29.243 176.437 5103 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.70 (0.23), residues: 1276 helix: 1.79 (0.18), residues: 773 sheet: 0.24 (0.70), residues: 55 loop : 0.18 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K1342 TYR 0.024 0.002 TYR A 99 PHE 0.029 0.002 PHE E 104 TRP 0.008 0.001 TRP K1466 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (18223) covalent geometry : angle 0.61056 / 0.35 (26005) hydrogen bonds : bond 0.05570 / 3.88 ( 865) hydrogen bonds : angle 3.66782 / 2.67 ( 2279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9138 (t0) cc_final: 0.8870 (m-30) REVERT: D 56 MET cc_start: 0.9351 (tmm) cc_final: 0.8988 (tpp) REVERT: K 1157 MET cc_start: 0.4381 (ttt) cc_final: 0.2887 (ttt) REVERT: K 1254 MET cc_start: 0.1269 (tpt) cc_final: -0.0761 (ptp) REVERT: K 1478 ARG cc_start: 0.5880 (mmp-170) cc_final: 0.5348 (tpm170) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1113 time to fit residues: 13.9151 Evaluate side-chains 51 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 116 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 125 GLN K1056 GLN ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1591 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.052265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.034876 restraints weight = 232742.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035451 restraints weight = 137969.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036130 restraints weight = 99339.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036389 restraints weight = 74616.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036581 restraints weight = 64106.874| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18223 Z= 0.261 Angle : 0.779 13.880 26005 Z= 0.432 Chirality : 0.044 0.357 2893 Planarity : 0.007 0.072 2182 Dihedral : 29.693 179.945 5103 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.23 (0.23), residues: 1276 helix: 1.41 (0.18), residues: 773 sheet: -0.12 (0.68), residues: 60 loop : 0.03 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 40 TYR 0.023 0.002 TYR B 51 PHE 0.026 0.003 PHE K1508 TRP 0.013 0.002 TRP K1466 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.26 (18223) covalent geometry : angle 0.77852 / 0.43 (26005) hydrogen bonds : bond 0.11145 / 7.63 ( 865) hydrogen bonds : angle 4.14642 / 3.02 ( 2279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9242 (t0) cc_final: 0.8854 (m-30) REVERT: B 84 MET cc_start: 0.9338 (ttp) cc_final: 0.8888 (tmm) REVERT: D 56 MET cc_start: 0.9326 (tmm) cc_final: 0.8963 (tpp) REVERT: E 41 TYR cc_start: 0.8610 (m-80) cc_final: 0.8300 (m-80) REVERT: K 1157 MET cc_start: 0.4268 (ttt) cc_final: 0.2843 (ttt) REVERT: K 1254 MET cc_start: 0.1536 (tpt) cc_final: -0.0482 (ptp) REVERT: K 1478 ARG cc_start: 0.5643 (mmp-170) cc_final: 0.5084 (tpm170) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1130 time to fit residues: 11.8501 Evaluate side-chains 50 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 8 optimal weight: 0.0970 chunk 130 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN K1261 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.053815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.036051 restraints weight = 227950.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036794 restraints weight = 127995.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.037476 restraints weight = 89255.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.037775 restraints weight = 66267.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037929 restraints weight = 56990.085| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18223 Z= 0.142 Angle : 0.619 10.596 26005 Z= 0.357 Chirality : 0.041 0.364 2893 Planarity : 0.005 0.058 2182 Dihedral : 29.683 179.295 5103 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.54 (0.23), residues: 1276 helix: 1.78 (0.18), residues: 766 sheet: -0.15 (0.67), residues: 60 loop : -0.04 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K1137 TYR 0.024 0.001 TYR A 99 PHE 0.018 0.001 PHE K1508 TRP 0.010 0.001 TRP K1649 HIS 0.011 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (18223) covalent geometry : angle 0.61897 / 0.36 (26005) hydrogen bonds : bond 0.05196 / 3.61 ( 865) hydrogen bonds : angle 3.73840 / 2.74 ( 2279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9139 (t0) cc_final: 0.8863 (m-30) REVERT: B 84 MET cc_start: 0.9285 (ttp) cc_final: 0.8814 (tmm) REVERT: D 56 MET cc_start: 0.9397 (tmm) cc_final: 0.9044 (tpp) REVERT: K 1157 MET cc_start: 0.4901 (ttt) cc_final: 0.3861 (ttt) REVERT: K 1254 MET cc_start: 0.1943 (tpt) cc_final: -0.0017 (ptp) REVERT: K 1288 PHE cc_start: 0.6946 (m-80) cc_final: 0.6721 (m-80) REVERT: K 1478 ARG cc_start: 0.5699 (mmp-170) cc_final: 0.5170 (tpm170) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1296 time to fit residues: 13.5569 Evaluate side-chains 49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 144 optimal weight: 0.3980 chunk 141 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN K1261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.053269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035741 restraints weight = 228384.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.036389 restraints weight = 128116.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037231 restraints weight = 86897.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037448 restraints weight = 64539.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037788 restraints weight = 56506.193| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18223 Z= 0.166 Angle : 0.640 10.170 26005 Z= 0.366 Chirality : 0.040 0.353 2893 Planarity : 0.005 0.059 2182 Dihedral : 29.704 179.003 5103 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.55 (0.23), residues: 1276 helix: 1.79 (0.18), residues: 765 sheet: -0.20 (0.67), residues: 60 loop : -0.05 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 134 TYR 0.022 0.002 TYR A 99 PHE 0.020 0.001 PHE K1508 TRP 0.009 0.001 TRP K1466 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (18223) covalent geometry : angle 0.64029 / 0.37 (26005) hydrogen bonds : bond 0.06340 / 4.38 ( 865) hydrogen bonds : angle 3.78306 / 2.76 ( 2279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9172 (t0) cc_final: 0.8869 (m-30) REVERT: B 84 MET cc_start: 0.9333 (ttp) cc_final: 0.8874 (tmm) REVERT: D 56 MET cc_start: 0.9355 (tmm) cc_final: 0.8952 (tpp) REVERT: K 1157 MET cc_start: 0.4475 (ttt) cc_final: 0.3584 (ttt) REVERT: K 1254 MET cc_start: 0.2449 (tpt) cc_final: 0.0451 (ptp) REVERT: K 1288 PHE cc_start: 0.6969 (m-80) cc_final: 0.6768 (m-80) REVERT: K 1478 ARG cc_start: 0.5683 (mmp-170) cc_final: 0.5180 (tpm170) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1318 time to fit residues: 14.1210 Evaluate side-chains 49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 73 optimal weight: 50.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN K1230 GLN K1261 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.050719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.033676 restraints weight = 204967.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.034866 restraints weight = 109366.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.035645 restraints weight = 71343.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.036137 restraints weight = 53388.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.036363 restraints weight = 43785.986| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18223 Z= 0.144 Angle : 0.614 8.458 26005 Z= 0.352 Chirality : 0.040 0.350 2893 Planarity : 0.005 0.057 2182 Dihedral : 29.695 179.592 5103 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.62 (0.23), residues: 1276 helix: 1.86 (0.18), residues: 766 sheet: -0.19 (0.65), residues: 60 loop : -0.03 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.022 0.001 TYR A 99 PHE 0.015 0.001 PHE K1508 TRP 0.011 0.001 TRP K1466 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (18223) covalent geometry : angle 0.61368 / 0.35 (26005) hydrogen bonds : bond 0.05013 / 3.49 ( 865) hydrogen bonds : angle 3.66477 / 2.67 ( 2279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9149 (ttp) cc_final: 0.8889 (tmm) REVERT: K 1124 MET cc_start: 0.7286 (ttm) cc_final: 0.7047 (ttp) REVERT: K 1157 MET cc_start: 0.4715 (ttt) cc_final: 0.3288 (ttt) REVERT: K 1254 MET cc_start: 0.1603 (tpt) cc_final: -0.0339 (ptp) REVERT: K 1288 PHE cc_start: 0.6618 (m-80) cc_final: 0.6394 (m-80) REVERT: K 1478 ARG cc_start: 0.5429 (mmp-170) cc_final: 0.4900 (tpm170) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1244 time to fit residues: 13.2189 Evaluate side-chains 49 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 114 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 overall best weight: 12.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 64 ASN G 38 ASN ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1307 ASN K1415 HIS K1464 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.047923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.031470 restraints weight = 248212.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.031908 restraints weight = 155491.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.032331 restraints weight = 108325.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.032587 restraints weight = 86669.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.032668 restraints weight = 74595.808| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.104 18223 Z= 0.467 Angle : 1.106 15.125 26005 Z= 0.593 Chirality : 0.059 0.366 2893 Planarity : 0.010 0.101 2182 Dihedral : 30.777 173.169 5103 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 39.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: -0.54 (0.22), residues: 1276 helix: -0.02 (0.17), residues: 781 sheet: -0.69 (0.70), residues: 54 loop : -0.71 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG E 40 TYR 0.033 0.004 TYR B 51 PHE 0.035 0.005 PHE H 62 TRP 0.028 0.004 TRP K1466 HIS 0.070 0.006 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00871 / 0.47 (18223) covalent geometry : angle 1.10575 / 0.59 (26005) hydrogen bonds : bond 0.19095 / 13.08 ( 865) hydrogen bonds : angle 5.36087 / 3.94 ( 2279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.9363 (ttp) cc_final: 0.8887 (tmm) REVERT: K 1288 PHE cc_start: 0.6555 (m-80) cc_final: 0.6174 (m-80) REVERT: K 1478 ARG cc_start: 0.5689 (mmp-170) cc_final: 0.5230 (tpm170) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1248 time to fit residues: 9.6709 Evaluate side-chains 42 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 64 ASN F 93 GLN K1663 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.033264 restraints weight = 237214.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.033908 restraints weight = 137301.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.034300 restraints weight = 93046.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.034864 restraints weight = 72997.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.034932 restraints weight = 60687.143| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18223 Z= 0.210 Angle : 0.753 8.657 26005 Z= 0.420 Chirality : 0.046 0.389 2893 Planarity : 0.006 0.058 2182 Dihedral : 30.978 179.329 5103 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.27 (0.22), residues: 1276 helix: 0.76 (0.18), residues: 772 sheet: -0.84 (0.68), residues: 54 loop : -0.56 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 39 TYR 0.029 0.002 TYR A 99 PHE 0.022 0.002 PHE K1508 TRP 0.016 0.002 TRP K1466 HIS 0.014 0.002 HIS K1415 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 (18223) covalent geometry : angle 0.75302 / 0.42 (26005) hydrogen bonds : bond 0.08265 / 5.61 ( 865) hydrogen bonds : angle 4.53593 / 3.36 ( 2279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7877 (mt) cc_final: 0.7605 (mt) REVERT: B 84 MET cc_start: 0.9464 (ttp) cc_final: 0.9137 (tmm) REVERT: K 1288 PHE cc_start: 0.6222 (m-80) cc_final: 0.5912 (m-80) REVERT: K 1478 ARG cc_start: 0.5901 (mmp-170) cc_final: 0.5472 (tpm170) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1097 time to fit residues: 10.9335 Evaluate side-chains 45 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 30.0000 chunk 118 optimal weight: 0.1980 chunk 145 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 142 optimal weight: 30.0000 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN K1236 ASN K1307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.047191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.029505 restraints weight = 228409.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.030415 restraints weight = 124977.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.031020 restraints weight = 86367.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031467 restraints weight = 67014.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.031672 restraints weight = 56032.061| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18223 Z= 0.190 Angle : 0.708 9.186 26005 Z= 0.396 Chirality : 0.043 0.388 2893 Planarity : 0.005 0.059 2182 Dihedral : 30.842 179.170 5103 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.73 (0.23), residues: 1276 helix: 1.18 (0.18), residues: 766 sheet: -0.95 (0.66), residues: 54 loop : -0.41 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 88 TYR 0.026 0.002 TYR A 99 PHE 0.021 0.002 PHE K1508 TRP 0.022 0.002 TRP K1466 HIS 0.010 0.002 HIS K1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.19 (18223) covalent geometry : angle 0.70800 / 0.40 (26005) hydrogen bonds : bond 0.07015 / 4.79 ( 865) hydrogen bonds : angle 4.33135 / 3.22 ( 2279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.58 seconds wall clock time: 52 minutes 38.52 seconds (3158.52 seconds total)