Starting phenix.real_space_refine on Wed Nov 15 09:31:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/11_2023/8q63_18183_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/11_2023/8q63_18183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/11_2023/8q63_18183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/11_2023/8q63_18183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/11_2023/8q63_18183_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q63_18183/11_2023/8q63_18183_updated.pdb" } resolution = 3.68 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= 0.001 sd= 0.010 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 70 5.49 5 S 35 5.16 5 C 7041 2.51 5 N 1971 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11346 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2698 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 309} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 7200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7200 Classifications: {'peptide': 915} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 44, 'TRANS': 870} Chain breaks: 4 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "N" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 642 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "T" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 630 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 152 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 6} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.40, per 1000 atoms: 0.74 Number of scatterers: 11346 At special positions: 0 Unit cell: (103.79, 116.4, 118.34, 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 35 16.00 P 70 15.00 O 2229 8.00 N 1971 7.00 C 7041 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.2 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 10 sheets defined 52.4% alpha, 6.8% beta 26 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 5.62 Creating SS restraints... Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 145 through 156 removed outlier: 4.090A pdb=" N ILE B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.602A pdb=" N LYS B 214 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 274 through 281 removed outlier: 4.141A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SER B 280 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU B 281 " --> pdb=" O VAL B 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 281' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.795A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 300' Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 398 through 420 removed outlier: 4.247A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 447 through 475 removed outlier: 4.291A pdb=" N LEU A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A 451 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.764A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 514 Processing helix chain 'A' and resid 531 through 551 removed outlier: 3.855A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 611 removed outlier: 3.747A pdb=" N VAL A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.628A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 777 through 812 Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 880 through 899 removed outlier: 4.028A pdb=" N LEU A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP A 893 " --> pdb=" O SER A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 910 Processing helix chain 'A' and resid 914 through 929 Processing helix chain 'A' and resid 933 through 935 No H-bonds generated for 'chain 'A' and resid 933 through 935' Processing helix chain 'A' and resid 949 through 958 removed outlier: 3.703A pdb=" N ALA A 956 " --> pdb=" O GLN A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 978 through 996 Processing helix chain 'A' and resid 999 through 1006 removed outlier: 4.974A pdb=" N ASP A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1022 removed outlier: 3.729A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1038 Processing helix chain 'A' and resid 1047 through 1065 removed outlier: 3.686A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS A1057 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A1060 " --> pdb=" O LYS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1084 Processing helix chain 'A' and resid 1090 through 1093 No H-bonds generated for 'chain 'A' and resid 1090 through 1093' Processing helix chain 'A' and resid 1150 through 1180 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1198 through 1214 Processing helix chain 'A' and resid 1217 through 1228 Processing helix chain 'A' and resid 1243 through 1259 removed outlier: 3.562A pdb=" N GLN A1246 " --> pdb=" O ASP A1243 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A1247 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A1254 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1280 removed outlier: 3.647A pdb=" N LEU A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1296 through 1302 removed outlier: 3.889A pdb=" N PHE A1300 " --> pdb=" O THR A1296 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A1302 " --> pdb=" O SER A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1309 No H-bonds generated for 'chain 'A' and resid 1306 through 1309' Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 4.376A pdb=" N ASN A1345 " --> pdb=" O THR A1341 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 49 through 53 removed outlier: 6.244A pdb=" N GLN B 72 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP B 52 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER B 74 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN B 96 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLU B 77 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU B 98 " --> pdb=" O GLU B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 134 through 137 removed outlier: 4.208A pdb=" N MET B 247 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 613 through 620 removed outlier: 3.937A pdb=" N ALA A 625 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 634 through 636 removed outlier: 3.547A pdb=" N ALA A 635 " --> pdb=" O LYS A 650 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= F, first strand: chain 'A' and resid 822 through 824 Processing sheet with id= G, first strand: chain 'A' and resid 942 through 944 Processing sheet with id= H, first strand: chain 'A' and resid 1109 through 1111 removed outlier: 3.739A pdb=" N TRP A1110 " --> pdb=" O ILE A1118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.610A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1233 through 1238 435 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1999 1.33 - 1.45: 3277 1.45 - 1.57: 6274 1.57 - 1.69: 146 1.69 - 1.82: 60 Bond restraints: 11756 Sorted by residual: bond pdb=" O3' DG N 136 " pdb=" P DC N 137 " ideal model delta sigma weight residual 1.607 1.449 0.158 1.50e-02 4.44e+03 1.11e+02 bond pdb=" C3' DC N 137 " pdb=" C2' DC N 137 " ideal model delta sigma weight residual 1.525 1.696 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sigma weight residual 1.610 1.492 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C2' DC N 137 " pdb=" C1' DC N 137 " ideal model delta sigma weight residual 1.525 1.409 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" O3' DC T 18 " pdb=" P DA T 19 " ideal model delta sigma weight residual 1.607 1.524 0.083 1.50e-02 4.44e+03 3.06e+01 ... (remaining 11751 not shown) Histogram of bond angle deviations from ideal: 91.54 - 100.07: 23 100.07 - 108.61: 1255 108.61 - 117.15: 7475 117.15 - 125.69: 7025 125.69 - 134.23: 449 Bond angle restraints: 16227 Sorted by residual: angle pdb=" O3' DG N 136 " pdb=" P DC N 137 " pdb=" O5' DC N 137 " ideal model delta sigma weight residual 104.00 124.80 -20.80 1.50e+00 4.44e-01 1.92e+02 angle pdb=" C3' DC T 18 " pdb=" O3' DC T 18 " pdb=" P DA T 19 " ideal model delta sigma weight residual 120.20 104.85 15.35 1.50e+00 4.44e-01 1.05e+02 angle pdb=" C3' DT T 20 " pdb=" O3' DT T 20 " pdb=" P DT T 21 " ideal model delta sigma weight residual 120.20 105.74 14.46 1.50e+00 4.44e-01 9.29e+01 angle pdb=" C2' DC N 137 " pdb=" C1' DC N 137 " pdb=" N1 DC N 137 " ideal model delta sigma weight residual 113.50 100.28 13.22 1.50e+00 4.44e-01 7.76e+01 angle pdb=" C3' DA N 131 " pdb=" O3' DA N 131 " pdb=" P DA N 132 " ideal model delta sigma weight residual 120.20 132.94 -12.74 1.50e+00 4.44e-01 7.22e+01 ... (remaining 16222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 6460 34.16 - 68.31: 332 68.31 - 102.47: 16 102.47 - 136.62: 1 136.62 - 170.78: 2 Dihedral angle restraints: 6811 sinusoidal: 3180 harmonic: 3631 Sorted by residual: dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -12.75 117.34 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" C5' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" O3' G C 108 " ideal model delta sinusoidal sigma weight residual 147.00 112.01 34.99 1 8.00e+00 1.56e-02 2.71e+01 dihedral pdb=" O4' G C 108 " pdb=" C4' G C 108 " pdb=" C3' G C 108 " pdb=" C2' G C 108 " ideal model delta sinusoidal sigma weight residual 24.00 -7.29 31.29 1 8.00e+00 1.56e-02 2.18e+01 ... (remaining 6808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1716 0.127 - 0.253: 36 0.253 - 0.380: 4 0.380 - 0.507: 17 0.507 - 0.633: 27 Chirality restraints: 1800 Sorted by residual: chirality pdb=" P DG T 10 " pdb=" OP1 DG T 10 " pdb=" OP2 DG T 10 " pdb=" O5' DG T 10 " both_signs ideal model delta sigma weight residual True 2.35 2.98 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DG N 108 " pdb=" OP1 DG N 108 " pdb=" OP2 DG N 108 " pdb=" O5' DG N 108 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.80e+00 chirality pdb=" P DC N 137 " pdb=" OP1 DC N 137 " pdb=" OP2 DC N 137 " pdb=" O5' DC N 137 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.57e+00 ... (remaining 1797 not shown) Planarity restraints: 1825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N 135 " 0.034 2.00e-02 2.50e+03 1.68e-02 7.09e+00 pdb=" N1 DT N 135 " -0.037 2.00e-02 2.50e+03 pdb=" C2 DT N 135 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT N 135 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DT N 135 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DT N 135 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT N 135 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DT N 135 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT N 135 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT N 135 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 159 " 0.017 2.00e-02 2.50e+03 1.60e-02 6.42e+00 pdb=" CG TRP B 159 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 159 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 159 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 159 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 159 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 159 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 159 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 159 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 159 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 320 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU B 320 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU B 320 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP B 321 " -0.011 2.00e-02 2.50e+03 ... (remaining 1822 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 291 2.68 - 3.23: 11140 3.23 - 3.79: 18617 3.79 - 4.34: 24683 4.34 - 4.90: 38384 Nonbonded interactions: 93115 Sorted by model distance: nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.121 2.440 nonbonded pdb=" OD1 ASP A 843 " pdb=" NE2 GLN A 916 " model vdw 2.205 2.520 nonbonded pdb=" O SER B 190 " pdb=" OG SER B 193 " model vdw 2.228 2.440 nonbonded pdb=" N LYS B 49 " pdb=" O LYS B 131 " model vdw 2.262 2.520 nonbonded pdb=" OD1 ASP A 876 " pdb=" NH1 ARG A 883 " model vdw 2.264 2.520 ... (remaining 93110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 0.090 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: 1.150 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 40.990 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 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 : 0.007 0.171 11756 Z= 0.391 Angle : 1.034 20.795 16227 Z= 0.537 Chirality : 0.094 0.633 1800 Planarity : 0.004 0.042 1825 Dihedral : 17.972 170.778 4457 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.09 % Allowed : 0.66 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1232 helix: 1.59 (0.21), residues: 666 sheet: -1.19 (0.56), residues: 80 loop : -1.01 (0.29), residues: 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.2182 time to fit residues: 56.8197 Evaluate side-chains 129 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 0.0970 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.0030 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 628 HIS A 642 ASN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11756 Z= 0.188 Angle : 0.608 8.092 16227 Z= 0.322 Chirality : 0.040 0.172 1800 Planarity : 0.004 0.046 1825 Dihedral : 18.430 174.909 2042 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.31 % Allowed : 9.01 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1232 helix: 1.53 (0.20), residues: 677 sheet: -1.37 (0.56), residues: 80 loop : -0.88 (0.29), residues: 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.301 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 165 average time/residue: 0.2358 time to fit residues: 57.3077 Evaluate side-chains 147 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1129 time to fit residues: 3.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 79 optimal weight: 0.0070 chunk 32 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS A 658 GLN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11756 Z= 0.256 Angle : 0.604 9.026 16227 Z= 0.315 Chirality : 0.040 0.142 1800 Planarity : 0.004 0.035 1825 Dihedral : 18.369 170.228 2042 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.60 % Allowed : 11.92 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1232 helix: 1.45 (0.21), residues: 670 sheet: -1.27 (0.57), residues: 80 loop : -0.80 (0.30), residues: 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 0.2431 time to fit residues: 53.2660 Evaluate side-chains 139 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1240 time to fit residues: 4.0078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN A 658 GLN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11756 Z= 0.245 Angle : 0.589 7.923 16227 Z= 0.308 Chirality : 0.040 0.134 1800 Planarity : 0.004 0.033 1825 Dihedral : 18.376 166.953 2042 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.41 % Allowed : 13.99 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1232 helix: 1.37 (0.21), residues: 664 sheet: -1.15 (0.57), residues: 80 loop : -0.77 (0.30), residues: 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.365 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 156 average time/residue: 0.2295 time to fit residues: 53.0425 Evaluate side-chains 140 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1529 time to fit residues: 3.4531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11756 Z= 0.288 Angle : 0.624 8.527 16227 Z= 0.323 Chirality : 0.041 0.163 1800 Planarity : 0.004 0.035 1825 Dihedral : 18.410 167.864 2042 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.50 % Allowed : 17.09 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1232 helix: 1.24 (0.21), residues: 662 sheet: -1.19 (0.57), residues: 80 loop : -0.81 (0.30), residues: 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 148 average time/residue: 0.2400 time to fit residues: 52.0662 Evaluate side-chains 142 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1146 time to fit residues: 3.5724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS ** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11756 Z= 0.214 Angle : 0.599 9.091 16227 Z= 0.308 Chirality : 0.039 0.151 1800 Planarity : 0.004 0.060 1825 Dihedral : 18.319 169.052 2042 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.13 % Allowed : 17.75 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1232 helix: 1.29 (0.21), residues: 660 sheet: -1.31 (0.52), residues: 90 loop : -0.66 (0.30), residues: 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.259 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 160 average time/residue: 0.2518 time to fit residues: 58.4095 Evaluate side-chains 142 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1001 time to fit residues: 2.3439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 76 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 11756 Z= 0.230 Angle : 0.612 9.782 16227 Z= 0.316 Chirality : 0.040 0.177 1800 Planarity : 0.004 0.055 1825 Dihedral : 18.298 169.221 2042 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.60 % Allowed : 18.50 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1232 helix: 1.24 (0.21), residues: 660 sheet: -1.24 (0.52), residues: 90 loop : -0.66 (0.30), residues: 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.314 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 154 average time/residue: 0.2379 time to fit residues: 53.4191 Evaluate side-chains 146 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.422 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1180 time to fit residues: 3.7778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN A1169 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11756 Z= 0.254 Angle : 0.642 11.978 16227 Z= 0.328 Chirality : 0.041 0.221 1800 Planarity : 0.004 0.049 1825 Dihedral : 18.315 169.443 2042 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.22 % Allowed : 19.25 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1232 helix: 1.18 (0.21), residues: 659 sheet: -1.20 (0.52), residues: 90 loop : -0.70 (0.30), residues: 483 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.325 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 143 average time/residue: 0.2492 time to fit residues: 51.7749 Evaluate side-chains 142 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1197 time to fit residues: 3.7667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 0.0970 chunk 35 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1070 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11756 Z= 0.229 Angle : 0.637 14.553 16227 Z= 0.325 Chirality : 0.041 0.213 1800 Planarity : 0.004 0.045 1825 Dihedral : 18.278 169.241 2042 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.75 % Allowed : 19.91 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1232 helix: 1.22 (0.21), residues: 654 sheet: -1.06 (0.52), residues: 92 loop : -0.65 (0.30), residues: 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.364 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 141 average time/residue: 0.2468 time to fit residues: 50.3278 Evaluate side-chains 137 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1231 time to fit residues: 2.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 85 optimal weight: 0.0270 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11756 Z= 0.232 Angle : 0.637 11.202 16227 Z= 0.327 Chirality : 0.041 0.233 1800 Planarity : 0.004 0.041 1825 Dihedral : 18.274 171.078 2042 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.28 % Allowed : 20.38 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1232 helix: 1.19 (0.21), residues: 654 sheet: -1.12 (0.52), residues: 92 loop : -0.62 (0.30), residues: 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.242 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 135 average time/residue: 0.2394 time to fit residues: 47.3249 Evaluate side-chains 135 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.242 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1167 time to fit residues: 2.3588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 15 optimal weight: 0.0020 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 0.1980 chunk 5 optimal weight: 0.0870 overall best weight: 2.0368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.152887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119739 restraints weight = 20275.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.123841 restraints weight = 10820.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.126510 restraints weight = 7376.943| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11756 Z= 0.187 Angle : 0.626 12.847 16227 Z= 0.319 Chirality : 0.041 0.260 1800 Planarity : 0.004 0.037 1825 Dihedral : 18.165 168.029 2042 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.56 % Allowed : 20.28 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1232 helix: 1.28 (0.21), residues: 651 sheet: -1.05 (0.53), residues: 94 loop : -0.44 (0.30), residues: 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.79 seconds wall clock time: 38 minutes 50.42 seconds (2330.42 seconds total)