Starting phenix.real_space_refine on Fri Mar 15 01:05:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfg_30663/03_2024/7dfg_30663_updated.pdb" } resolution = 2.7 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= 0.006 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 33 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 6383 2.51 5 N 1707 2.21 5 O 2023 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 29": "OD1" <-> "OD2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ASP 736": "OD1" <-> "OD2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 804": "OD1" <-> "OD2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "G ASP 112": "OD1" <-> "OD2" Residue "G PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ASP 175": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10223 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "T" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 908, 7327 Classifications: {'peptide': 908} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 877} Chain breaks: 2 Chain: "B" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "P" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'1RP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Unusual residues: {' MG': 4, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3015 SG CYS A 301 52.303 65.210 44.160 1.00 27.60 S ATOM 3056 SG CYS A 306 52.362 64.611 40.300 1.00 26.32 S ATOM 3088 SG CYS A 310 55.984 64.395 42.479 1.00 25.33 S ATOM 4496 SG CYS A 487 33.869 59.947 52.053 1.00 32.69 S ATOM 5749 SG CYS A 645 33.137 59.771 47.959 1.00 36.88 S ATOM 5755 SG CYS A 646 36.211 62.001 49.701 1.00 34.30 S Time building chain proxies: 5.89, per 1000 atoms: 0.58 Number of scatterers: 10223 At special positions: 0 Unit cell: (112.245, 93.003, 130.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 33 15.00 Mg 4 11.99 F 1 9.00 O 2023 8.00 N 1707 7.00 C 6383 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: 3.94 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 8 sheets defined 42.5% alpha, 12.4% beta 10 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.731A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.685A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 199 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.088A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.432A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.670A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.956A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.972A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 579 removed outlier: 3.954A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.741A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 895 removed outlier: 4.223A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 919 through 925 removed outlier: 3.904A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 removed outlier: 3.971A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 removed outlier: 4.313A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 39 removed outlier: 3.999A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.990A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 98 Processing helix chain 'G' and resid 101 through 111 removed outlier: 3.520A pdb=" N ARG G 111 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 141 Processing helix chain 'G' and resid 174 through 177 No H-bonds generated for 'chain 'G' and resid 174 through 177' Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.539A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.495A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.606A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= F, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.336A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 128 through 132 removed outlier: 6.491A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2071 1.32 - 1.45: 2662 1.45 - 1.57: 5593 1.57 - 1.69: 59 1.69 - 1.81: 105 Bond restraints: 10490 Sorted by residual: bond pdb=" C3' 1RP P1201 " pdb=" C4' 1RP P1201 " ideal model delta sigma weight residual 1.336 1.532 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C4' 1RP P1201 " pdb=" O4' 1RP P1201 " ideal model delta sigma weight residual 1.645 1.453 0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" C5' 1RP P1201 " pdb=" O5' 1RP P1201 " ideal model delta sigma weight residual 1.416 1.600 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" CAQ 1RP P1201 " pdb=" CAR 1RP P1201 " ideal model delta sigma weight residual 1.535 1.383 0.152 2.00e-02 2.50e+03 5.81e+01 bond pdb=" O5' 1RP P1201 " pdb=" PAX 1RP P1201 " ideal model delta sigma weight residual 1.678 1.527 0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 10485 not shown) Histogram of bond angle deviations from ideal: 95.17 - 102.96: 131 102.96 - 110.75: 3558 110.75 - 118.54: 4647 118.54 - 126.34: 5832 126.34 - 134.13: 202 Bond angle restraints: 14370 Sorted by residual: angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 102.60 95.17 7.43 1.00e+00 1.00e+00 5.52e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 124.05 -10.35 1.50e+00 4.44e-01 4.77e+01 angle pdb=" O5' U P 20 " pdb=" C5' U P 20 " pdb=" C4' U P 20 " ideal model delta sigma weight residual 111.50 101.26 10.24 1.50e+00 4.44e-01 4.66e+01 angle pdb=" C3' A P 19 " pdb=" O3' A P 19 " pdb=" P U P 20 " ideal model delta sigma weight residual 120.20 130.35 -10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" C3' U P 20 " pdb=" C2' U P 20 " pdb=" O2' U P 20 " ideal model delta sigma weight residual 110.70 119.47 -8.77 1.50e+00 4.44e-01 3.42e+01 ... (remaining 14365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 5996 27.68 - 55.35: 224 55.35 - 83.02: 39 83.02 - 110.70: 1 110.70 - 138.37: 1 Dihedral angle restraints: 6261 sinusoidal: 2701 harmonic: 3560 Sorted by residual: dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual 180.00 -139.61 -40.39 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" O4 POP A1003 " pdb=" O POP A1003 " pdb=" P2 POP A1003 " pdb=" P1 POP A1003 " ideal model delta sinusoidal sigma weight residual -57.41 80.96 -138.37 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" CA TRP G 182 " pdb=" C TRP G 182 " pdb=" N PRO G 183 " pdb=" CA PRO G 183 " ideal model delta harmonic sigma weight residual -180.00 -152.93 -27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 6258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1470 0.097 - 0.193: 167 0.193 - 0.290: 5 0.290 - 0.386: 2 0.386 - 0.482: 1 Chirality restraints: 1645 Sorted by residual: chirality pdb=" C4' U P 20 " pdb=" C5' U P 20 " pdb=" O4' U P 20 " pdb=" C3' U P 20 " both_signs ideal model delta sigma weight residual False -2.50 -2.01 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C3' U P 20 " pdb=" C4' U P 20 " pdb=" O3' U P 20 " pdb=" C2' U P 20 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C2' U P 20 " pdb=" C3' U P 20 " pdb=" O2' U P 20 " pdb=" C1' U P 20 " both_signs ideal model delta sigma weight residual False -2.75 -2.44 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1642 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 243 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 927 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 115 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO B 116 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " -0.030 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 125 2.63 - 3.20: 8530 3.20 - 3.76: 16635 3.76 - 4.33: 24088 4.33 - 4.90: 37855 Nonbonded interactions: 87233 Sorted by model distance: nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1007 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP A 218 " pdb="MG MG A1008 " model vdw 2.090 2.170 nonbonded pdb=" O6 POP A1006 " pdb="MG MG A1007 " model vdw 2.099 2.170 nonbonded pdb=" O2 POP A1006 " pdb="MG MG A1007 " model vdw 2.150 2.170 nonbonded pdb=" OG SER A 239 " pdb=" OD1 ASP A 465 " model vdw 2.259 2.440 ... (remaining 87228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 179 or resid 182 through 191)) selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 4.320 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.100 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.012 0.196 10490 Z= 0.765 Angle : 0.964 10.355 14370 Z= 0.536 Chirality : 0.062 0.482 1645 Planarity : 0.007 0.060 1728 Dihedral : 14.752 138.374 3957 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.38 % Allowed : 5.64 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.02 (0.19), residues: 1186 helix: -2.39 (0.16), residues: 541 sheet: -1.27 (0.38), residues: 150 loop : -1.56 (0.23), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP G 154 HIS 0.019 0.002 HIS A 613 PHE 0.032 0.004 PHE A 741 TYR 0.020 0.003 TYR A 867 ARG 0.009 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 1.218 Fit side-chains REVERT: A 224 GLN cc_start: 0.8415 (tt0) cc_final: 0.8193 (tt0) REVERT: A 424 VAL cc_start: 0.8858 (m) cc_final: 0.8657 (t) REVERT: A 761 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8187 (m-30) REVERT: B 176 ASN cc_start: 0.8083 (t0) cc_final: 0.7600 (t0) REVERT: C 27 LYS cc_start: 0.8518 (ttpt) cc_final: 0.8296 (ttmt) REVERT: C 51 LYS cc_start: 0.8376 (mttp) cc_final: 0.8167 (mttm) outliers start: 4 outliers final: 3 residues processed: 167 average time/residue: 1.1868 time to fit residues: 213.6425 Evaluate side-chains 146 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 39 ASN A 57 GLN A 75 HIS A 113 HIS A 117 GLN A 191 GLN A 256 HIS A 468 GLN A 507 ASN A 541 GLN A 611 ASN A 691 ASN A 705 ASN A 713 ASN A 773 GLN A 790 ASN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 179 ASN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10490 Z= 0.157 Angle : 0.477 6.644 14370 Z= 0.259 Chirality : 0.040 0.159 1645 Planarity : 0.004 0.040 1728 Dihedral : 10.991 123.910 1733 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.97 % Allowed : 11.56 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.32 (0.22), residues: 1186 helix: -0.70 (0.21), residues: 536 sheet: -0.95 (0.38), residues: 149 loop : -0.84 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 916 HIS 0.003 0.001 HIS A 613 PHE 0.016 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.004 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 138 ASN cc_start: 0.7291 (t0) cc_final: 0.7058 (t0) REVERT: B 176 ASN cc_start: 0.7934 (t0) cc_final: 0.7564 (t0) REVERT: G 101 ASP cc_start: 0.7438 (p0) cc_final: 0.7228 (p0) REVERT: G 117 LEU cc_start: 0.6156 (mm) cc_final: 0.5895 (mm) outliers start: 21 outliers final: 8 residues processed: 166 average time/residue: 1.1659 time to fit residues: 209.3941 Evaluate side-chains 150 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 57 GLN A 75 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 790 ASN A 886 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10490 Z= 0.152 Angle : 0.454 6.377 14370 Z= 0.244 Chirality : 0.040 0.163 1645 Planarity : 0.003 0.040 1728 Dihedral : 10.682 105.023 1729 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.97 % Allowed : 14.38 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.74 (0.23), residues: 1186 helix: -0.19 (0.22), residues: 549 sheet: -0.81 (0.38), residues: 151 loop : -0.53 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 613 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.006 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7478 (mmm160) cc_final: 0.6777 (mmm-85) REVERT: A 138 ASN cc_start: 0.7352 (t0) cc_final: 0.7141 (t0) REVERT: A 333 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 340 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.5550 (t80) REVERT: A 424 VAL cc_start: 0.8708 (t) cc_final: 0.8454 (m) REVERT: A 889 ARG cc_start: 0.7817 (tpt-90) cc_final: 0.7579 (tpt-90) REVERT: B 176 ASN cc_start: 0.7838 (t0) cc_final: 0.7535 (t0) outliers start: 21 outliers final: 10 residues processed: 160 average time/residue: 1.1306 time to fit residues: 196.4288 Evaluate side-chains 155 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 75 HIS ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 886 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10490 Z= 0.125 Angle : 0.428 6.116 14370 Z= 0.228 Chirality : 0.039 0.159 1645 Planarity : 0.003 0.031 1728 Dihedral : 10.405 88.842 1729 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.07 % Allowed : 15.13 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.32 (0.24), residues: 1186 helix: 0.13 (0.22), residues: 552 sheet: -0.53 (0.40), residues: 136 loop : -0.33 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.003 0.001 HIS A 892 PHE 0.013 0.001 PHE A 741 TYR 0.012 0.001 TYR A 788 ARG 0.004 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 92 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7166 (p0) REVERT: A 105 ARG cc_start: 0.7471 (mmm160) cc_final: 0.7149 (tpt170) REVERT: A 138 ASN cc_start: 0.7440 (t0) cc_final: 0.7209 (t0) REVERT: A 340 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.5394 (t80) REVERT: A 424 VAL cc_start: 0.8817 (t) cc_final: 0.8600 (m) REVERT: A 833 ASP cc_start: 0.7544 (t70) cc_final: 0.7336 (t70) REVERT: A 889 ARG cc_start: 0.7802 (tpt-90) cc_final: 0.7581 (tpt-90) REVERT: B 176 ASN cc_start: 0.7818 (t0) cc_final: 0.7531 (t0) REVERT: G 101 ASP cc_start: 0.6954 (p0) cc_final: 0.6745 (p0) REVERT: G 117 LEU cc_start: 0.6034 (mm) cc_final: 0.5741 (mm) outliers start: 22 outliers final: 7 residues processed: 171 average time/residue: 1.0690 time to fit residues: 198.5176 Evaluate side-chains 156 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 790 ASN A 886 GLN A 892 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN C 19 GLN C 34 GLN C 36 HIS C 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10490 Z= 0.269 Angle : 0.497 7.089 14370 Z= 0.263 Chirality : 0.042 0.157 1645 Planarity : 0.003 0.032 1728 Dihedral : 10.412 75.324 1729 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.29 % Allowed : 14.29 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.32 (0.23), residues: 1186 helix: 0.18 (0.22), residues: 543 sheet: -0.76 (0.38), residues: 151 loop : -0.28 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 154 HIS 0.003 0.001 HIS A 892 PHE 0.019 0.002 PHE A 741 TYR 0.016 0.002 TYR A 788 ARG 0.003 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 138 ASN cc_start: 0.7561 (t0) cc_final: 0.7280 (t0) REVERT: A 226 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 340 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.5764 (t80) REVERT: A 424 VAL cc_start: 0.8792 (t) cc_final: 0.8536 (m) REVERT: A 924 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8177 (mmm) REVERT: B 176 ASN cc_start: 0.7842 (t0) cc_final: 0.7436 (t0) outliers start: 35 outliers final: 16 residues processed: 160 average time/residue: 1.1276 time to fit residues: 195.2062 Evaluate side-chains 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 81 GLN A 541 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 886 GLN A 892 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10490 Z= 0.261 Angle : 0.491 6.938 14370 Z= 0.261 Chirality : 0.042 0.156 1645 Planarity : 0.003 0.034 1728 Dihedral : 10.245 73.475 1727 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.20 % Allowed : 15.70 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.20 (0.23), residues: 1186 helix: 0.25 (0.22), residues: 546 sheet: -0.63 (0.38), residues: 145 loop : -0.22 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 154 HIS 0.002 0.001 HIS A 752 PHE 0.019 0.002 PHE A 741 TYR 0.014 0.002 TYR A 867 ARG 0.008 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 138 ASN cc_start: 0.7465 (t0) cc_final: 0.7198 (t0) REVERT: A 226 THR cc_start: 0.8469 (OUTLIER) cc_final: 0.8121 (p) REVERT: A 340 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.5636 (t80) REVERT: A 424 VAL cc_start: 0.8806 (t) cc_final: 0.8574 (m) REVERT: A 924 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8184 (mmm) REVERT: B 176 ASN cc_start: 0.7852 (t0) cc_final: 0.7455 (t0) REVERT: G 90 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7817 (ptp) outliers start: 34 outliers final: 21 residues processed: 161 average time/residue: 1.1205 time to fit residues: 195.6995 Evaluate side-chains 164 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 81 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 886 GLN A 892 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 34 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10490 Z= 0.158 Angle : 0.446 6.384 14370 Z= 0.238 Chirality : 0.040 0.152 1645 Planarity : 0.003 0.034 1728 Dihedral : 10.058 73.467 1727 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.63 % Allowed : 16.45 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.04 (0.24), residues: 1186 helix: 0.45 (0.22), residues: 545 sheet: -0.44 (0.40), residues: 136 loop : -0.14 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.002 0.000 HIS A 309 PHE 0.013 0.001 PHE A 741 TYR 0.012 0.001 TYR A 788 ARG 0.002 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.415 Fit side-chains REVERT: A 81 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: A 105 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7145 (tpt90) REVERT: A 226 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8106 (p) REVERT: A 340 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.5568 (t80) REVERT: A 833 ASP cc_start: 0.7588 (t70) cc_final: 0.7384 (t70) REVERT: A 889 ARG cc_start: 0.7682 (tmt90) cc_final: 0.7463 (tmt90) REVERT: B 176 ASN cc_start: 0.7834 (t0) cc_final: 0.7546 (t0) REVERT: G 90 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7854 (ptp) outliers start: 28 outliers final: 16 residues processed: 159 average time/residue: 1.1249 time to fit residues: 193.8356 Evaluate side-chains 159 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 81 GLN A 138 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 886 GLN A 892 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10490 Z= 0.157 Angle : 0.452 6.451 14370 Z= 0.242 Chirality : 0.039 0.152 1645 Planarity : 0.003 0.033 1728 Dihedral : 10.037 73.485 1727 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.44 % Allowed : 17.39 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.11 (0.24), residues: 1186 helix: 0.51 (0.22), residues: 545 sheet: -0.37 (0.41), residues: 134 loop : -0.11 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.002 0.000 HIS A 82 PHE 0.014 0.001 PHE A 741 TYR 0.012 0.001 TYR A 788 ARG 0.003 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 1.216 Fit side-chains REVERT: A 8 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 105 ARG cc_start: 0.7440 (mmm160) cc_final: 0.7147 (tpt90) REVERT: A 340 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.5560 (t80) REVERT: A 833 ASP cc_start: 0.7591 (t70) cc_final: 0.7376 (t70) REVERT: A 889 ARG cc_start: 0.7682 (tmt90) cc_final: 0.7474 (tmt90) REVERT: B 176 ASN cc_start: 0.7838 (t0) cc_final: 0.7554 (t0) REVERT: G 90 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7839 (ptp) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 1.1181 time to fit residues: 182.7532 Evaluate side-chains 160 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 64 optimal weight: 0.0870 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 138 ASN A 790 ASN A 886 GLN A 892 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN C 19 GLN C 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10490 Z= 0.140 Angle : 0.444 6.017 14370 Z= 0.237 Chirality : 0.039 0.151 1645 Planarity : 0.003 0.032 1728 Dihedral : 9.997 73.464 1727 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.07 % Allowed : 18.14 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.20 (0.24), residues: 1186 helix: 0.57 (0.23), residues: 545 sheet: -0.36 (0.41), residues: 134 loop : -0.03 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.001 0.000 HIS C 36 PHE 0.013 0.001 PHE A 741 TYR 0.011 0.001 TYR A 788 ARG 0.002 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.170 Fit side-chains REVERT: A 8 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 105 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7175 (tpt90) REVERT: A 226 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 340 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.5598 (t80) REVERT: A 833 ASP cc_start: 0.7584 (t70) cc_final: 0.7364 (t70) REVERT: B 176 ASN cc_start: 0.7835 (t0) cc_final: 0.7555 (t0) REVERT: G 90 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7839 (ptp) outliers start: 22 outliers final: 14 residues processed: 148 average time/residue: 1.1004 time to fit residues: 176.6595 Evaluate side-chains 152 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Chi-restraints excluded: chain G residue 94 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 138 ASN A 572 HIS ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN A 886 GLN A 892 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10490 Z= 0.303 Angle : 0.515 6.849 14370 Z= 0.272 Chirality : 0.042 0.146 1645 Planarity : 0.003 0.033 1728 Dihedral : 10.248 73.451 1727 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.26 % Allowed : 18.05 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.06 (0.24), residues: 1186 helix: 0.32 (0.22), residues: 541 sheet: -0.50 (0.38), residues: 141 loop : -0.11 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 154 HIS 0.002 0.001 HIS A 752 PHE 0.020 0.002 PHE A 741 TYR 0.016 0.002 TYR A 867 ARG 0.002 0.000 ARG B 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.138 Fit side-chains REVERT: A 8 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7731 (tt) REVERT: A 340 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.5762 (t80) REVERT: B 176 ASN cc_start: 0.7849 (t0) cc_final: 0.7466 (t0) REVERT: G 90 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7853 (ptp) outliers start: 24 outliers final: 12 residues processed: 150 average time/residue: 1.1223 time to fit residues: 182.7898 Evaluate side-chains 150 residues out of total 1064 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 90 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 790 ASN A 886 GLN A 892 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097238 restraints weight = 12467.219| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.81 r_work: 0.3016 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10490 Z= 0.151 Angle : 0.453 6.008 14370 Z= 0.243 Chirality : 0.039 0.148 1645 Planarity : 0.003 0.032 1728 Dihedral : 10.041 73.456 1727 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.79 % Allowed : 18.98 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.15 (0.24), residues: 1186 helix: 0.52 (0.23), residues: 546 sheet: -0.35 (0.41), residues: 134 loop : -0.05 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.001 0.000 HIS A 113 PHE 0.013 0.001 PHE A 741 TYR 0.018 0.001 TYR G 138 ARG 0.002 0.000 ARG A 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3792.10 seconds wall clock time: 67 minutes 43.94 seconds (4063.94 seconds total)