Starting phenix.real_space_refine on Thu Feb 15 18:00:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qee_4536/02_2024/6qee_4536_updated.pdb" } resolution = 3.9 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 8388 2.51 5 N 2131 2.21 5 O 2396 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 94": "NH1" <-> "NH2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A ASP 177": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A ASP 520": "OD1" <-> "OD2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 805": "OD1" <-> "OD2" Residue "A ARG 831": "NH1" <-> "NH2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 971": "OE1" <-> "OE2" Residue "A ASP 996": "OD1" <-> "OD2" Residue "A GLU 1058": "OE1" <-> "OE2" Residue "A TYR 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C ARG 222": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12975 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9184 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 27, 'TRANS': 1154} Chain breaks: 1 Chain: "B" Number of atoms: 1713 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} bond proxies already assigned to first conformer: 1747 Chain: "C" Number of atoms: 1720 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Conformer: "B" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} bond proxies already assigned to first conformer: 1763 Chain: "A" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 358 Unusual residues: {'3PE': 1, 'CLR': 7, 'NAG': 3, 'ZQU': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.63, per 1000 atoms: 0.67 Number of scatterers: 12975 At special positions: 0 Unit cell: (178.08, 134.4, 145.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 1 15.00 F 4 9.00 O 2396 8.00 N 2131 7.00 C 8388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG BCYS C 204 " distance=2.08 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=0, symmetry=0 Links applied NAG-ASN " NAG A1401 " - " ASN A 93 " " NAG A1402 " - " ASN A 90 " " NAG A1403 " - " ASN A 98 " Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.9 seconds 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3002 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 13 sheets defined 44.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 35 through 38 No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 45 through 61 removed outlier: 3.772A pdb=" N LEU A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 89 removed outlier: 3.670A pdb=" N GLY A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 155 removed outlier: 3.568A pdb=" N PHE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TRP A 135 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.686A pdb=" N VAL A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.577A pdb=" N ILE A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 209 Processing helix chain 'A' and resid 211 through 236 removed outlier: 3.876A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 247 through 256 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.547A pdb=" N ALA A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 270 through 319 removed outlier: 4.212A pdb=" N ASN A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 346 Processing helix chain 'A' and resid 349 through 369 removed outlier: 4.223A pdb=" N PHE A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 440 removed outlier: 4.445A pdb=" N GLN A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.662A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 545 Processing helix chain 'A' and resid 562 through 574 removed outlier: 3.694A pdb=" N ALA A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 593 No H-bonds generated for 'chain 'A' and resid 590 through 593' Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 696 through 703 removed outlier: 4.060A pdb=" N ASN A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 720 removed outlier: 4.453A pdb=" N VAL A 712 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 719 " --> pdb=" O PHE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 744 through 796 removed outlier: 3.636A pdb=" N PHE A 776 " --> pdb=" O GLN A 772 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 783 " --> pdb=" O ALA A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 804 Processing helix chain 'A' and resid 810 through 818 Processing helix chain 'A' and resid 821 through 824 No H-bonds generated for 'chain 'A' and resid 821 through 824' Processing helix chain 'A' and resid 829 through 851 removed outlier: 4.271A pdb=" N GLY A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 878 removed outlier: 4.330A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Proline residue: A 865 - end of helix Processing helix chain 'A' and resid 885 through 887 No H-bonds generated for 'chain 'A' and resid 885 through 887' Processing helix chain 'A' and resid 891 through 901 removed outlier: 3.886A pdb=" N ILE A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 901 " --> pdb=" O THR A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 909 Processing helix chain 'A' and resid 912 through 965 removed outlier: 3.770A pdb=" N SER A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 4.112A pdb=" N ILE A 939 " --> pdb=" O HIS A 935 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 952 " --> pdb=" O MET A 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 965 " --> pdb=" O TYR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 removed outlier: 5.164A pdb=" N ALA A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1011 Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1105 through 1110 Processing helix chain 'A' and resid 1126 through 1133 removed outlier: 4.890A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1151 removed outlier: 3.542A pdb=" N ALA A1151 " --> pdb=" O ALA A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1158 Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1210 through 1220 Processing helix chain 'A' and resid 1256 through 1261 Processing helix chain 'A' and resid 1265 through 1274 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing sheet with id= A, first strand: chain 'A' and resid 422 through 425 removed outlier: 5.975A pdb=" N VAL A 596 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 425 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA A 598 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 599 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 607 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 552 through 554 removed outlier: 6.263A pdb=" N ILE A 582 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 1064 through 1066 removed outlier: 5.924A pdb=" N CYS A1226 " --> pdb=" O LEU A1065 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 19 through 23 removed outlier: 3.513A pdb=" N ALA B 19 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 77 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.124A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.697A pdb=" N ASN B 143 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 139 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 150 through 156 removed outlier: 3.641A pdb=" N ASN B 151 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 203 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 213 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.828A pdb=" N GLN C 5 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 18 through 21 removed outlier: 3.623A pdb=" N VAL C 18 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 116 through 118 removed outlier: 3.562A pdb=" N ILE C 34 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.593A pdb=" N LYS C 152 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 178 through 180 Processing sheet with id= M, first strand: chain 'C' and resid 206 through 208 540 hydrogen bonds defined for protein. 1571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 5.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2090 1.31 - 1.46: 4932 1.46 - 1.61: 6156 1.61 - 1.76: 3 1.76 - 1.90: 89 Bond restraints: 13270 Sorted by residual: bond pdb=" C06 ZQU A1405 " pdb=" C08 ZQU A1405 " ideal model delta sigma weight residual 1.662 1.515 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C7 NAG A1403 " pdb=" N2 NAG A1403 " ideal model delta sigma weight residual 1.346 1.488 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C06 ZQU A1404 " pdb=" C08 ZQU A1404 " ideal model delta sigma weight residual 1.662 1.522 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C7 NAG A1402 " pdb=" N2 NAG A1402 " ideal model delta sigma weight residual 1.346 1.483 -0.137 2.00e-02 2.50e+03 4.70e+01 bond pdb=" C7 NAG A1401 " pdb=" N2 NAG A1401 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.48e+01 ... (remaining 13265 not shown) Histogram of bond angle deviations from ideal: 59.48 - 74.53: 6 74.53 - 89.59: 0 89.59 - 104.64: 237 104.64 - 119.70: 11579 119.70 - 134.76: 6199 Bond angle restraints: 18021 Sorted by residual: angle pdb=" C03 ZQU A1404 " pdb=" C01 ZQU A1404 " pdb=" C04 ZQU A1404 " ideal model delta sigma weight residual 58.20 119.00 -60.80 3.00e+00 1.11e-01 4.11e+02 angle pdb=" C03 ZQU A1405 " pdb=" C01 ZQU A1405 " pdb=" C04 ZQU A1405 " ideal model delta sigma weight residual 58.20 117.36 -59.16 3.00e+00 1.11e-01 3.89e+02 angle pdb=" O12 3PE A1413 " pdb=" P 3PE A1413 " pdb=" O14 3PE A1413 " ideal model delta sigma weight residual 123.79 100.57 23.22 3.00e+00 1.11e-01 5.99e+01 angle pdb=" C03 ZQU A1404 " pdb=" C02 ZQU A1404 " pdb=" C05 ZQU A1404 " ideal model delta sigma weight residual 138.97 116.35 22.62 3.00e+00 1.11e-01 5.68e+01 angle pdb=" C03 ZQU A1405 " pdb=" C02 ZQU A1405 " pdb=" C05 ZQU A1405 " ideal model delta sigma weight residual 138.97 117.27 21.70 3.00e+00 1.11e-01 5.23e+01 ... (remaining 18016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 7638 23.34 - 46.68: 528 46.68 - 70.03: 66 70.03 - 93.37: 15 93.37 - 116.71: 2 Dihedral angle restraints: 8249 sinusoidal: 3563 harmonic: 4686 Sorted by residual: dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual 180.00 131.98 48.02 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA LYS B 55 " pdb=" C LYS B 55 " pdb=" N VAL B 56 " pdb=" CA VAL B 56 " ideal model delta harmonic sigma weight residual -180.00 -132.19 -47.81 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG BCYS C 204 " pdb=" CB BCYS C 204 " ideal model delta sinusoidal sigma weight residual 93.00 156.16 -63.16 1 1.00e+01 1.00e-02 5.27e+01 ... (remaining 8246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.542: 2066 0.542 - 1.085: 5 1.085 - 1.627: 0 1.627 - 2.169: 0 2.169 - 2.711: 1 Chirality restraints: 2072 Sorted by residual: chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 0.31 -2.71 2.00e-01 2.50e+01 1.84e+02 chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A 93 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" C01 ZQU A1405 " pdb=" C02 ZQU A1405 " pdb=" C03 ZQU A1405 " pdb=" C04 ZQU A1405 " both_signs ideal model delta sigma weight residual True 1.33 2.38 -1.05 2.00e-01 2.50e+01 2.75e+01 ... (remaining 2069 not shown) Planarity restraints: 2230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 93 " 0.139 2.00e-02 2.50e+03 1.64e-01 3.36e+02 pdb=" CG ASN A 93 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 93 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN A 93 " -0.264 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 90 " -0.148 2.00e-02 2.50e+03 1.59e-01 3.14e+02 pdb=" CG ASN A 90 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN A 90 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 90 " 0.266 2.00e-02 2.50e+03 pdb=" C1 NAG A1402 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.048 2.00e-02 2.50e+03 1.20e-01 1.79e+02 pdb=" CG ASN A 98 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " -0.072 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.222 2.00e-02 2.50e+03 pdb=" C1 NAG A1403 " -0.121 2.00e-02 2.50e+03 ... (remaining 2227 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2273 2.76 - 3.29: 11903 3.29 - 3.83: 20917 3.83 - 4.36: 23146 4.36 - 4.90: 40758 Nonbonded interactions: 98997 Sorted by model distance: nonbonded pdb=" OG SER A1125 " pdb=" OE1 GLU A1128 " model vdw 2.223 2.440 nonbonded pdb=" O ASP A 96 " pdb=" OG1 THR A 100 " model vdw 2.231 2.440 nonbonded pdb=" O LYS B 155 " pdb=" OG1 THR B 199 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 25 " pdb=" N SER B 26 " model vdw 2.291 2.520 nonbonded pdb=" NH2 ARG A 275 " pdb=" OD1 ASP A1123 " model vdw 2.294 2.520 ... (remaining 98992 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=0.46 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 14.010 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 39.470 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.011 0.151 13270 Z= 0.747 Angle : 1.488 60.796 18021 Z= 0.672 Chirality : 0.105 2.711 2072 Planarity : 0.008 0.100 2227 Dihedral : 15.383 116.710 5235 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 1.09 % Allowed : 5.18 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -4.04 (0.16), residues: 1621 helix: -2.61 (0.13), residues: 763 sheet: -2.22 (0.31), residues: 248 loop : -2.71 (0.20), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 102 HIS 0.007 0.002 HIS A 611 PHE 0.029 0.003 PHE A 731 TYR 0.025 0.003 TYR A 952 ARG 0.018 0.001 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7067 (mtt) cc_final: 0.6716 (mtt) REVERT: A 156 ASN cc_start: 0.8586 (t0) cc_final: 0.8286 (t0) REVERT: A 615 MET cc_start: 0.7563 (mmm) cc_final: 0.6313 (tpt) REVERT: A 715 PHE cc_start: 0.8353 (t80) cc_final: 0.7824 (t80) REVERT: C 89 GLU cc_start: 0.7656 (mp0) cc_final: 0.7404 (mp0) outliers start: 13 outliers final: 8 residues processed: 157 average time/residue: 0.2577 time to fit residues: 59.0562 Evaluate side-chains 97 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A1154 HIS A1181 GLN ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 ASN A1256 HIS B 6 GLN B 31 HIS B 143 ASN B 144 ASN B 162 GLN B 172 GLN B 204 HIS B 216 ASN C 31 ASN C 39 GLN C 102 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13270 Z= 0.239 Angle : 0.754 14.916 18021 Z= 0.357 Chirality : 0.048 0.574 2072 Planarity : 0.005 0.079 2227 Dihedral : 9.263 70.642 2344 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % Rotamer: Outliers : 1.82 % Allowed : 11.89 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -2.37 (0.19), residues: 1621 helix: -0.82 (0.17), residues: 770 sheet: -1.67 (0.33), residues: 232 loop : -2.38 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 102 HIS 0.004 0.001 HIS A 60 PHE 0.024 0.002 PHE A 398 TYR 0.023 0.002 TYR A 927 ARG 0.005 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7895 (m-30) cc_final: 0.7691 (m-30) REVERT: A 156 ASN cc_start: 0.8336 (t0) cc_final: 0.8007 (t0) REVERT: A 478 LEU cc_start: 0.7705 (tp) cc_final: 0.7205 (tt) REVERT: A 615 MET cc_start: 0.7569 (mmm) cc_final: 0.6530 (tpt) REVERT: A 715 PHE cc_start: 0.8316 (t80) cc_final: 0.7731 (t80) REVERT: A 861 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8793 (mp) REVERT: A 877 MET cc_start: 0.8180 (tmm) cc_final: 0.7846 (tmt) REVERT: A 948 MET cc_start: 0.7623 (ttm) cc_final: 0.7352 (ttm) REVERT: A 1191 ARG cc_start: 0.6863 (ttm-80) cc_final: 0.6514 (tpp80) REVERT: B 219 GLU cc_start: 0.7777 (pm20) cc_final: 0.6961 (pm20) outliers start: 23 outliers final: 14 residues processed: 118 average time/residue: 0.2529 time to fit residues: 44.6278 Evaluate side-chains 108 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.0770 chunk 122 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN A1152 ASN A1154 HIS ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13270 Z= 0.199 Angle : 0.705 15.091 18021 Z= 0.326 Chirality : 0.048 0.595 2072 Planarity : 0.004 0.077 2227 Dihedral : 8.471 68.034 2340 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.26 % Allowed : 13.57 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -1.52 (0.20), residues: 1621 helix: 0.07 (0.18), residues: 764 sheet: -1.56 (0.33), residues: 250 loop : -2.10 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS A 611 PHE 0.015 0.001 PHE B 92 TYR 0.020 0.002 TYR A 927 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 GLU cc_start: 0.6624 (tp30) cc_final: 0.6379 (tp30) REVERT: A 478 LEU cc_start: 0.7735 (tp) cc_final: 0.7248 (tt) REVERT: A 615 MET cc_start: 0.7576 (mmm) cc_final: 0.6385 (tpt) REVERT: A 715 PHE cc_start: 0.8287 (t80) cc_final: 0.7669 (t80) REVERT: A 948 MET cc_start: 0.7524 (ttm) cc_final: 0.7250 (ttm) REVERT: C 202 ILE cc_start: 0.8386 (tp) cc_final: 0.8065 (pt) outliers start: 29 outliers final: 18 residues processed: 125 average time/residue: 0.2390 time to fit residues: 45.4499 Evaluate side-chains 107 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 76 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 98 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 720 ASN A1152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13270 Z= 0.164 Angle : 0.672 14.787 18021 Z= 0.308 Chirality : 0.047 0.579 2072 Planarity : 0.004 0.073 2227 Dihedral : 7.982 66.281 2339 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.77 % Allowed : 15.39 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.99 (0.21), residues: 1621 helix: 0.54 (0.19), residues: 765 sheet: -1.26 (0.34), residues: 239 loop : -1.90 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.004 0.000 HIS A 611 PHE 0.015 0.001 PHE A 334 TYR 0.021 0.001 TYR A 927 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: A 467 GLU cc_start: 0.6659 (tp30) cc_final: 0.6393 (tp30) REVERT: A 478 LEU cc_start: 0.7688 (tp) cc_final: 0.7195 (tt) REVERT: A 615 MET cc_start: 0.7530 (mmm) cc_final: 0.6431 (tpt) REVERT: A 715 PHE cc_start: 0.8275 (t80) cc_final: 0.7585 (t80) REVERT: A 948 MET cc_start: 0.7522 (ttm) cc_final: 0.7240 (ttm) REVERT: A 1067 LEU cc_start: 0.8132 (mm) cc_final: 0.7805 (mt) REVERT: B 219 GLU cc_start: 0.7658 (pm20) cc_final: 0.6879 (pm20) REVERT: C 202 ILE cc_start: 0.8338 (tp) cc_final: 0.8074 (pt) outliers start: 36 outliers final: 20 residues processed: 126 average time/residue: 0.2381 time to fit residues: 45.8107 Evaluate side-chains 110 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A1194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13270 Z= 0.177 Angle : 0.680 14.812 18021 Z= 0.310 Chirality : 0.047 0.583 2072 Planarity : 0.004 0.074 2227 Dihedral : 7.760 66.817 2339 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.55 % Allowed : 16.41 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.73 (0.21), residues: 1621 helix: 0.73 (0.19), residues: 770 sheet: -1.27 (0.33), residues: 256 loop : -1.67 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.006 0.001 HIS A 611 PHE 0.028 0.001 PHE A 398 TYR 0.021 0.001 TYR A 927 ARG 0.004 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7648 (m-30) cc_final: 0.7426 (m-30) REVERT: A 110 MET cc_start: 0.8839 (tpp) cc_final: 0.8240 (tpp) REVERT: A 203 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: A 467 GLU cc_start: 0.6632 (tp30) cc_final: 0.6364 (tp30) REVERT: A 615 MET cc_start: 0.7458 (mmm) cc_final: 0.6480 (tpt) REVERT: A 948 MET cc_start: 0.7488 (ttm) cc_final: 0.7230 (ttm) REVERT: A 1067 LEU cc_start: 0.8077 (mm) cc_final: 0.7738 (mt) REVERT: A 1164 TYR cc_start: 0.4690 (m-10) cc_final: 0.4171 (p90) REVERT: B 219 GLU cc_start: 0.7681 (pm20) cc_final: 0.6913 (pm20) REVERT: C 202 ILE cc_start: 0.8342 (tp) cc_final: 0.8113 (pt) outliers start: 33 outliers final: 24 residues processed: 124 average time/residue: 0.2368 time to fit residues: 44.9228 Evaluate side-chains 115 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 10.0000 chunk 141 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13270 Z= 0.238 Angle : 0.720 14.988 18021 Z= 0.333 Chirality : 0.049 0.600 2072 Planarity : 0.004 0.074 2227 Dihedral : 7.829 68.654 2339 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.63 % Allowed : 17.29 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.70 (0.21), residues: 1621 helix: 0.67 (0.19), residues: 768 sheet: -1.06 (0.34), residues: 249 loop : -1.62 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 102 HIS 0.006 0.001 HIS A 611 PHE 0.032 0.001 PHE A 334 TYR 0.021 0.002 TYR A 927 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7800 (m-30) cc_final: 0.7518 (m-30) REVERT: A 467 GLU cc_start: 0.6635 (tp30) cc_final: 0.6364 (tp30) REVERT: A 478 LEU cc_start: 0.7685 (tp) cc_final: 0.7217 (tt) REVERT: A 614 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.5018 (mm) REVERT: A 615 MET cc_start: 0.7378 (mmm) cc_final: 0.6468 (tpt) REVERT: A 626 MET cc_start: 0.7382 (ttp) cc_final: 0.7038 (tpp) REVERT: A 948 MET cc_start: 0.7481 (ttm) cc_final: 0.7260 (ttm) REVERT: A 1164 TYR cc_start: 0.4792 (m-10) cc_final: 0.4207 (p90) REVERT: B 219 GLU cc_start: 0.7648 (pm20) cc_final: 0.6838 (pm20) outliers start: 35 outliers final: 25 residues processed: 121 average time/residue: 0.2282 time to fit residues: 42.5651 Evaluate side-chains 114 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 87 optimal weight: 0.2980 chunk 156 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13270 Z= 0.182 Angle : 0.697 14.853 18021 Z= 0.317 Chirality : 0.049 0.597 2072 Planarity : 0.004 0.072 2227 Dihedral : 7.709 66.842 2339 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.41 % Allowed : 17.80 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.50 (0.21), residues: 1621 helix: 0.87 (0.19), residues: 767 sheet: -1.00 (0.34), residues: 245 loop : -1.56 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.007 0.001 HIS A 611 PHE 0.036 0.001 PHE A 334 TYR 0.022 0.001 TYR A 927 ARG 0.004 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8605 (tpt) cc_final: 0.8405 (tpt) REVERT: A 93 ASN cc_start: 0.3801 (p0) cc_final: 0.3549 (m110) REVERT: A 266 PHE cc_start: 0.8002 (m-80) cc_final: 0.7761 (t80) REVERT: A 467 GLU cc_start: 0.6625 (tp30) cc_final: 0.6359 (tp30) REVERT: A 478 LEU cc_start: 0.7681 (tp) cc_final: 0.7218 (tt) REVERT: A 614 LEU cc_start: 0.5335 (OUTLIER) cc_final: 0.4972 (mm) REVERT: A 948 MET cc_start: 0.7537 (ttm) cc_final: 0.7289 (ttm) REVERT: A 1164 TYR cc_start: 0.4729 (m-10) cc_final: 0.4192 (p90) REVERT: B 219 GLU cc_start: 0.7684 (pm20) cc_final: 0.6950 (pm20) outliers start: 32 outliers final: 27 residues processed: 120 average time/residue: 0.2932 time to fit residues: 54.4038 Evaluate side-chains 114 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13270 Z= 0.168 Angle : 0.684 14.755 18021 Z= 0.311 Chirality : 0.048 0.579 2072 Planarity : 0.004 0.072 2227 Dihedral : 7.567 66.134 2339 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.48 % Allowed : 17.43 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.37 (0.21), residues: 1621 helix: 0.98 (0.19), residues: 767 sheet: -0.89 (0.34), residues: 245 loop : -1.53 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.006 0.000 HIS A 611 PHE 0.046 0.001 PHE A 334 TYR 0.021 0.001 TYR A 927 ARG 0.003 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 94 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LEU cc_start: 0.7686 (tp) cc_final: 0.7239 (tt) REVERT: A 1164 TYR cc_start: 0.4784 (m-10) cc_final: 0.4251 (p90) REVERT: B 219 GLU cc_start: 0.7628 (pm20) cc_final: 0.6922 (pm20) outliers start: 33 outliers final: 29 residues processed: 123 average time/residue: 0.2274 time to fit residues: 42.9792 Evaluate side-chains 113 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 84 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13270 Z= 0.177 Angle : 0.908 59.198 18021 Z= 0.461 Chirality : 0.048 0.580 2072 Planarity : 0.004 0.073 2227 Dihedral : 7.594 66.029 2339 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.48 % Allowed : 17.65 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.34 (0.21), residues: 1621 helix: 0.99 (0.19), residues: 767 sheet: -0.84 (0.34), residues: 245 loop : -1.50 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 47 HIS 0.011 0.001 HIS A 611 PHE 0.022 0.001 PHE A 334 TYR 0.021 0.001 TYR A 927 ARG 0.005 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7946 (mmt) cc_final: 0.7733 (mmt) REVERT: A 88 MET cc_start: 0.6609 (mmp) cc_final: 0.5963 (mpp) REVERT: A 478 LEU cc_start: 0.7711 (tp) cc_final: 0.7254 (tt) REVERT: A 614 LEU cc_start: 0.5294 (OUTLIER) cc_final: 0.4904 (mm) REVERT: A 1164 TYR cc_start: 0.4770 (m-10) cc_final: 0.4249 (p90) REVERT: B 219 GLU cc_start: 0.7626 (pm20) cc_final: 0.6928 (pm20) outliers start: 33 outliers final: 31 residues processed: 112 average time/residue: 0.2299 time to fit residues: 39.9465 Evaluate side-chains 116 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 106 optimal weight: 0.0050 chunk 161 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13270 Z= 0.177 Angle : 0.908 59.198 18021 Z= 0.461 Chirality : 0.048 0.580 2072 Planarity : 0.004 0.073 2227 Dihedral : 7.594 66.029 2339 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.41 % Allowed : 17.72 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.34 (0.21), residues: 1621 helix: 0.99 (0.19), residues: 767 sheet: -0.84 (0.34), residues: 245 loop : -1.50 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 47 HIS 0.011 0.001 HIS A 611 PHE 0.022 0.001 PHE A 334 TYR 0.021 0.001 TYR A 927 ARG 0.005 0.000 ARG A 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7946 (mmt) cc_final: 0.7733 (mmt) REVERT: A 88 MET cc_start: 0.6611 (mmp) cc_final: 0.5963 (mpp) REVERT: A 478 LEU cc_start: 0.7711 (tp) cc_final: 0.7254 (tt) REVERT: A 614 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.4904 (mm) REVERT: A 1164 TYR cc_start: 0.4770 (m-10) cc_final: 0.4249 (p90) REVERT: B 219 GLU cc_start: 0.7626 (pm20) cc_final: 0.6928 (pm20) outliers start: 32 outliers final: 31 residues processed: 111 average time/residue: 0.2289 time to fit residues: 39.6109 Evaluate side-chains 116 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 84 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 400 TYR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 509 TYR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 927 TYR Chi-restraints excluded: chain A residue 956 PHE Chi-restraints excluded: chain A residue 971 GLU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1041 PHE Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 83 PHE Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 0.0980 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.109567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.091154 restraints weight = 55190.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091980 restraints weight = 93123.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092695 restraints weight = 34481.979| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13270 Z= 0.177 Angle : 0.908 59.198 18021 Z= 0.461 Chirality : 0.048 0.580 2072 Planarity : 0.004 0.073 2227 Dihedral : 7.594 66.029 2339 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.41 % Allowed : 17.72 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.06 % Twisted Proline : 1.96 % Twisted General : 0.06 % 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: -0.34 (0.21), residues: 1621 helix: 0.99 (0.19), residues: 767 sheet: -0.84 (0.34), residues: 245 loop : -1.50 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 47 HIS 0.011 0.001 HIS A 611 PHE 0.022 0.001 PHE A 334 TYR 0.021 0.001 TYR A 927 ARG 0.005 0.000 ARG A 592 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2717.93 seconds wall clock time: 50 minutes 35.69 seconds (3035.69 seconds total)