Starting phenix.real_space_refine on Mon Nov 18 18:22:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/11_2024/8haj_34592.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/11_2024/8haj_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/11_2024/8haj_34592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/11_2024/8haj_34592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/11_2024/8haj_34592.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8haj_34592/11_2024/8haj_34592.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 9.52, per 1000 atoms: 0.55 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: 4.00 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 7.08 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: 9.40 Time building geometry restraints manager: 4.66 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=" NZ ALY B 16 " pdb=" CH ALY B 16 " ideal model delta sigma weight residual 1.343 1.384 -0.041 2.00e-02 2.50e+03 4.31e+00 bond pdb=" NZ ALY B 12 " pdb=" CH ALY B 12 " ideal model delta sigma weight residual 1.343 1.383 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C LEU K1073 " pdb=" N PRO K1074 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.19e-02 7.06e+03 2.15e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CG GLU D 68 " pdb=" CD GLU D 68 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.69e+00 ... (remaining 18218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 25364 1.73 - 3.46: 569 3.46 - 5.20: 53 5.20 - 6.93: 15 6.93 - 8.66: 4 Bond angle restraints: 26005 Sorted by residual: angle pdb=" N GLU D 68 " pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " ideal model delta sigma weight residual 110.28 116.27 -5.99 1.55e+00 4.16e-01 1.49e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 110.77 118.16 -7.39 1.93e+00 2.68e-01 1.47e+01 angle pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta sigma weight residual 123.08 119.54 3.54 1.01e+00 9.80e-01 1.23e+01 angle pdb=" CA MET K1254 " pdb=" CB MET K1254 " pdb=" CG MET K1254 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " pdb=" CG GLU D 68 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.22e+00 ... (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: 2064 0.030 - 0.060: 608 0.060 - 0.091: 149 0.091 - 0.121: 61 0.121 - 0.151: 11 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=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" P DA J 60 " pdb=" OP1 DA J 60 " pdb=" OP2 DA J 60 " pdb=" O5' DA J 60 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.35e-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: 0.980 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: 0.050 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 44.500 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18223 Z= 0.167 Angle : 0.604 8.661 26005 Z= 0.369 Chirality : 0.034 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 : 11.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (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 TRP 0.011 0.001 TRP K1466 HIS 0.004 0.001 HIS E 113 PHE 0.020 0.001 PHE K1508 TYR 0.011 0.001 TYR K1117 ARG 0.012 0.000 ARG D 69 *********************** 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 : 1.540 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: 0.2666 time to fit residues: 40.3201 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 : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1132 ASN K1236 ASN K1261 HIS K1661 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18223 Z= 0.194 Angle : 0.558 7.019 26005 Z= 0.327 Chirality : 0.035 0.148 2893 Planarity : 0.005 0.058 2182 Dihedral : 28.271 167.466 5103 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.18 % Allowed : 2.22 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.23), residues: 1276 helix: 1.92 (0.19), residues: 774 sheet: 0.18 (0.62), residues: 65 loop : 0.18 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K1466 HIS 0.011 0.001 HIS E 113 PHE 0.017 0.001 PHE K1508 TYR 0.015 0.001 TYR F 72 ARG 0.005 0.000 ARG K1055 *********************** 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 87 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9266 (tp30) cc_final: 0.8826 (tt0) REVERT: A 106 ASP cc_start: 0.8888 (t0) cc_final: 0.8613 (m-30) REVERT: E 67 PHE cc_start: 0.8790 (t80) cc_final: 0.8309 (t80) REVERT: E 92 LEU cc_start: 0.9456 (mp) cc_final: 0.9173 (tt) REVERT: G 78 ILE cc_start: 0.9239 (mt) cc_final: 0.8936 (mm) REVERT: G 89 ASN cc_start: 0.9287 (m-40) cc_final: 0.8967 (m-40) REVERT: H 99 LEU cc_start: 0.9109 (tp) cc_final: 0.8845 (tp) REVERT: K 1478 ARG cc_start: 0.4825 (mmp-170) cc_final: 0.3971 (tpm170) REVERT: K 1505 GLU cc_start: 0.8138 (tt0) cc_final: 0.7907 (pt0) outliers start: 2 outliers final: 2 residues processed: 85 average time/residue: 0.2610 time to fit residues: 35.7208 Evaluate side-chains 63 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 0.0000 chunk 143 optimal weight: 0.0170 chunk 155 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN K1261 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18223 Z= 0.166 Angle : 0.535 6.759 26005 Z= 0.313 Chirality : 0.034 0.156 2893 Planarity : 0.004 0.057 2182 Dihedral : 28.380 169.872 5103 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1276 helix: 2.05 (0.18), residues: 773 sheet: 0.12 (0.60), residues: 66 loop : 0.18 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1466 HIS 0.005 0.001 HIS E 113 PHE 0.018 0.001 PHE K1508 TYR 0.016 0.001 TYR G 39 ARG 0.004 0.000 ARG K1055 *********************** 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 85 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9266 (tp30) cc_final: 0.8766 (tt0) REVERT: B 63 GLU cc_start: 0.8645 (pm20) cc_final: 0.8257 (pm20) REVERT: C 112 GLN cc_start: 0.7847 (mm110) cc_final: 0.6743 (mt0) REVERT: G 78 ILE cc_start: 0.9199 (mt) cc_final: 0.8917 (mm) REVERT: H 99 LEU cc_start: 0.9105 (tp) cc_final: 0.8823 (tp) REVERT: K 1122 TRP cc_start: 0.8299 (t-100) cc_final: 0.8076 (t60) REVERT: K 1157 MET cc_start: -0.1303 (ttt) cc_final: -0.1588 (ttt) REVERT: K 1254 MET cc_start: -0.1888 (tpt) cc_final: -0.3780 (ptp) REVERT: K 1478 ARG cc_start: 0.4768 (mmp-170) cc_final: 0.4025 (tpm170) REVERT: K 1505 GLU cc_start: 0.8201 (tt0) cc_final: 0.7972 (pt0) REVERT: K 1654 MET cc_start: 0.5429 (mmp) cc_final: 0.5009 (tpp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2673 time to fit residues: 36.8021 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 : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.0770 chunk 108 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN K1227 ASN K1236 ASN K1379 GLN K1638 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 18223 Z= 0.332 Angle : 0.672 7.996 26005 Z= 0.387 Chirality : 0.039 0.204 2893 Planarity : 0.006 0.058 2182 Dihedral : 28.941 169.145 5103 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1276 helix: 1.74 (0.18), residues: 772 sheet: 0.61 (0.70), residues: 55 loop : 0.25 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K1466 HIS 0.010 0.002 HIS G 82 PHE 0.022 0.002 PHE D 62 TYR 0.034 0.002 TYR K1585 ARG 0.006 0.001 ARG E 40 *********************** 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 75 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.535 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8879 (pm20) cc_final: 0.8345 (pm20) REVERT: E 41 TYR cc_start: 0.8102 (m-80) cc_final: 0.7748 (m-80) REVERT: K 1157 MET cc_start: -0.1186 (ttt) cc_final: -0.1455 (ttt) REVERT: K 1254 MET cc_start: -0.1057 (tpt) cc_final: -0.3728 (ptp) REVERT: K 1478 ARG cc_start: 0.4948 (mmp-170) cc_final: 0.4317 (tpm170) REVERT: K 1505 GLU cc_start: 0.8290 (tt0) cc_final: 0.8090 (pt0) REVERT: K 1624 MET cc_start: -0.1150 (mmt) cc_final: -0.1657 (mmt) REVERT: K 1652 MET cc_start: 0.7361 (tmm) cc_final: 0.7052 (ppp) REVERT: K 1654 MET cc_start: 0.6599 (mmp) cc_final: 0.5372 (mtt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2592 time to fit residues: 31.6870 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 : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN K1591 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18223 Z= 0.310 Angle : 0.662 7.638 26005 Z= 0.384 Chirality : 0.039 0.227 2893 Planarity : 0.006 0.057 2182 Dihedral : 29.651 175.358 5103 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.27 % Allowed : 2.93 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1276 helix: 1.65 (0.18), residues: 771 sheet: 0.07 (0.66), residues: 60 loop : 0.08 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K1466 HIS 0.008 0.002 HIS D 106 PHE 0.035 0.002 PHE E 104 TYR 0.028 0.002 TYR B 51 ARG 0.005 0.001 ARG K1104 *********************** 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 75 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: K 1157 MET cc_start: -0.0002 (ttt) cc_final: -0.0441 (ttt) REVERT: K 1254 MET cc_start: -0.0523 (tpt) cc_final: -0.2597 (ptp) REVERT: K 1478 ARG cc_start: 0.5032 (mmp-170) cc_final: 0.4380 (tpm170) REVERT: K 1654 MET cc_start: 0.7040 (mmp) cc_final: 0.6728 (tpp) outliers start: 3 outliers final: 0 residues processed: 73 average time/residue: 0.2882 time to fit residues: 33.0446 Evaluate side-chains 53 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 37 optimal weight: 0.0870 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN K1261 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18223 Z= 0.191 Angle : 0.595 9.599 26005 Z= 0.344 Chirality : 0.036 0.183 2893 Planarity : 0.004 0.054 2182 Dihedral : 29.540 173.459 5103 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1276 helix: 1.89 (0.18), residues: 769 sheet: 0.01 (0.65), residues: 60 loop : -0.03 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1466 HIS 0.004 0.001 HIS F 75 PHE 0.020 0.001 PHE K1508 TYR 0.024 0.002 TYR A 99 ARG 0.004 0.000 ARG K1137 *********************** 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 72 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8919 (pm20) cc_final: 0.8564 (pm20) REVERT: D 56 MET cc_start: 0.9550 (tmm) cc_final: 0.9098 (tpp) REVERT: K 1157 MET cc_start: 0.0255 (ttt) cc_final: -0.0248 (ttt) REVERT: K 1254 MET cc_start: -0.0730 (tpt) cc_final: -0.2645 (ptp) REVERT: K 1288 PHE cc_start: 0.6935 (m-80) cc_final: 0.6548 (m-10) REVERT: K 1478 ARG cc_start: 0.4947 (mmp-170) cc_final: 0.4370 (tpm170) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2764 time to fit residues: 32.0075 Evaluate side-chains 52 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN K1261 HIS ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18223 Z= 0.260 Angle : 0.635 15.004 26005 Z= 0.363 Chirality : 0.037 0.177 2893 Planarity : 0.005 0.056 2182 Dihedral : 29.530 170.946 5103 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.23), residues: 1276 helix: 1.89 (0.18), residues: 769 sheet: 0.04 (0.64), residues: 60 loop : -0.09 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K1466 HIS 0.006 0.002 HIS K1415 PHE 0.021 0.002 PHE K1508 TYR 0.023 0.002 TYR A 99 ARG 0.005 0.000 ARG G 35 *********************** 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 64 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: K 1157 MET cc_start: 0.0652 (ttt) cc_final: 0.0019 (ttt) REVERT: K 1254 MET cc_start: -0.0414 (tpt) cc_final: -0.2423 (ptp) REVERT: K 1288 PHE cc_start: 0.6136 (m-80) cc_final: 0.5886 (m-80) REVERT: K 1478 ARG cc_start: 0.4988 (mmp-170) cc_final: 0.4407 (tpm170) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3140 time to fit residues: 32.2320 Evaluate side-chains 52 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18223 Z= 0.302 Angle : 0.663 10.188 26005 Z= 0.381 Chirality : 0.038 0.184 2893 Planarity : 0.005 0.057 2182 Dihedral : 29.903 171.931 5103 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1276 helix: 1.73 (0.18), residues: 769 sheet: -0.05 (0.66), residues: 60 loop : -0.17 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1466 HIS 0.010 0.002 HIS E 39 PHE 0.020 0.002 PHE K1508 TYR 0.027 0.002 TYR A 99 ARG 0.004 0.001 ARG A 40 *********************** 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 62 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: K 1157 MET cc_start: 0.1788 (ttt) cc_final: 0.0966 (ttm) REVERT: K 1254 MET cc_start: 0.0098 (tpt) cc_final: -0.1986 (ptp) REVERT: K 1288 PHE cc_start: 0.5883 (m-80) cc_final: 0.5413 (m-80) REVERT: K 1478 ARG cc_start: 0.5155 (mmp-170) cc_final: 0.4647 (tpm170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2853 time to fit residues: 28.7609 Evaluate side-chains 47 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18223 Z= 0.278 Angle : 0.657 12.297 26005 Z= 0.375 Chirality : 0.038 0.202 2893 Planarity : 0.005 0.055 2182 Dihedral : 30.051 172.808 5103 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.23), residues: 1276 helix: 1.58 (0.18), residues: 771 sheet: -0.15 (0.66), residues: 60 loop : -0.24 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K1466 HIS 0.006 0.002 HIS K1262 PHE 0.020 0.002 PHE K1508 TYR 0.026 0.002 TYR A 99 ARG 0.007 0.001 ARG C 20 *********************** 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 60 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.572 Fit side-chains REVERT: B 84 MET cc_start: 0.9271 (ttp) cc_final: 0.8702 (tmm) REVERT: D 56 MET cc_start: 0.9450 (tmm) cc_final: 0.9087 (tpp) REVERT: K 1157 MET cc_start: 0.2605 (ttt) cc_final: 0.1684 (ttm) REVERT: K 1254 MET cc_start: 0.0927 (tpt) cc_final: -0.0926 (ptp) REVERT: K 1288 PHE cc_start: 0.5855 (m-80) cc_final: 0.5562 (m-10) REVERT: K 1470 MET cc_start: 0.5459 (mtp) cc_final: 0.5236 (mtm) REVERT: K 1478 ARG cc_start: 0.5119 (mmp-170) cc_final: 0.4669 (tpm170) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2816 time to fit residues: 27.7805 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 : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN ** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18223 Z= 0.303 Angle : 0.672 11.708 26005 Z= 0.383 Chirality : 0.039 0.200 2893 Planarity : 0.005 0.056 2182 Dihedral : 30.207 172.309 5103 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.23), residues: 1276 helix: 1.55 (0.18), residues: 769 sheet: -0.16 (0.67), residues: 54 loop : -0.31 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K1466 HIS 0.007 0.002 HIS K1255 PHE 0.020 0.002 PHE K1508 TYR 0.025 0.002 TYR A 99 ARG 0.005 0.001 ARG C 42 ********************** 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 59 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.606 Fit side-chains REVERT: B 84 MET cc_start: 0.9269 (ttp) cc_final: 0.8688 (tmm) REVERT: D 56 MET cc_start: 0.9440 (tmm) cc_final: 0.9062 (tpp) REVERT: K 1157 MET cc_start: 0.3100 (ttt) cc_final: 0.2051 (ttm) REVERT: K 1254 MET cc_start: 0.1179 (tpt) cc_final: -0.0893 (ptp) REVERT: K 1288 PHE cc_start: 0.6088 (m-80) cc_final: 0.5676 (m-80) REVERT: K 1470 MET cc_start: 0.4011 (mtp) cc_final: 0.3786 (mtp) REVERT: K 1478 ARG cc_start: 0.5084 (mmp-170) cc_final: 0.4698 (tpm170) REVERT: K 1652 MET cc_start: 0.7781 (tmm) cc_final: 0.7565 (tmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2605 time to fit residues: 26.0668 Evaluate side-chains 46 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1236 ASN ** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.051446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034185 restraints weight = 231155.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034918 restraints weight = 132446.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.035352 restraints weight = 88005.341| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18223 Z= 0.194 Angle : 0.615 9.709 26005 Z= 0.351 Chirality : 0.036 0.188 2893 Planarity : 0.004 0.053 2182 Dihedral : 30.103 174.078 5103 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1276 helix: 1.75 (0.18), residues: 769 sheet: 0.13 (0.69), residues: 54 loop : -0.22 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K1466 HIS 0.005 0.001 HIS K1255 PHE 0.033 0.002 PHE K1374 TYR 0.024 0.002 TYR A 99 ARG 0.005 0.000 ARG K1137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.22 seconds wall clock time: 45 minutes 4.81 seconds (2704.81 seconds total)