Starting phenix.real_space_refine on Wed Feb 14 08:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ctt_30469/02_2024/7ctt_30469_updated.pdb" } resolution = 3.2 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= 0.002 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 37 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5548 2.51 5 N 1492 2.21 5 O 1770 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 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ASP 736": "OD1" <-> "OD2" Residue "A ARG 750": "NH1" <-> "NH2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 879": "OD1" <-> "OD2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 919": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "D ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6610 Classifications: {'peptide': 826} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 28, 'TRANS': 797} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 856 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "Q" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'RNA': 16} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 9} Link IDs: {'rna3p': 15} Chain: "T" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 384 Classifications: {'RNA': 18} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'GE6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1801 SG CYS A 301 70.372 57.844 32.268 1.00 49.99 S ATOM 1842 SG CYS A 306 70.771 56.913 28.427 1.00 47.23 S ATOM 1874 SG CYS A 310 73.351 56.249 31.282 1.00 45.07 S ATOM 3267 SG CYS A 487 51.270 58.877 37.590 1.00 56.43 S ATOM 4520 SG CYS A 645 50.345 58.349 33.598 1.00 59.56 S ATOM 4526 SG CYS A 646 53.921 59.698 35.506 1.00 56.53 S Time building chain proxies: 5.29, per 1000 atoms: 0.59 Number of scatterers: 8912 At special positions: 0 Unit cell: (112, 90, 104, 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 61 16.00 P 37 15.00 Mg 1 11.99 F 1 9.00 O 1770 8.00 N 1492 7.00 C 5548 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=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " 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 ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 6 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 7 sheets defined 44.4% alpha, 8.1% beta 16 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.561A pdb=" N THR A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) 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 198 removed outlier: 3.725A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (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: 3.905A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.471A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 255' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' 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 317 removed outlier: 3.805A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.675A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.207A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.899A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' 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 572 removed outlier: 3.665A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 639 Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' 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 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 853 through 871 removed outlier: 3.776A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.669A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 889 removed outlier: 4.253A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.879A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.972A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 3 through 20 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: 3.912A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.829A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 101 through 110 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 334 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 347 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.856A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 5.687A 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 removed outlier: 3.703A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 819 through 821 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.440A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1387 1.32 - 1.44: 2752 1.44 - 1.56: 4869 1.56 - 1.69: 74 1.69 - 1.81: 94 Bond restraints: 9176 Sorted by residual: bond pdb=" C10 GE6 A1004 " pdb=" O05 GE6 A1004 " ideal model delta sigma weight residual 1.187 1.491 -0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C01 GE6 A1004 " pdb=" C04 GE6 A1004 " ideal model delta sigma weight residual 1.350 1.585 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 GE6 A1004 " pdb=" O01 GE6 A1004 " ideal model delta sigma weight residual 1.510 1.287 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C01 GE6 A1004 " pdb=" C02 GE6 A1004 " ideal model delta sigma weight residual 1.675 1.488 0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C10 GE6 A1004 " pdb=" N02 GE6 A1004 " ideal model delta sigma weight residual 1.462 1.323 0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.05: 328 106.05 - 113.03: 5015 113.03 - 120.01: 3189 120.01 - 126.99: 3942 126.99 - 133.98: 154 Bond angle restraints: 12628 Sorted by residual: angle pdb=" N SER A 682 " pdb=" CA SER A 682 " pdb=" C SER A 682 " ideal model delta sigma weight residual 113.28 109.71 3.57 1.22e+00 6.72e-01 8.56e+00 angle pdb=" C SER A 607 " pdb=" N ASP A 608 " pdb=" CA ASP A 608 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.55e+00 angle pdb=" C VAL A 335 " pdb=" N ASP A 336 " pdb=" CA ASP A 336 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.29e+00 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 126.61 -5.07 1.91e+00 2.74e-01 7.04e+00 angle pdb=" O THR A 556 " pdb=" C THR A 556 " pdb=" N VAL A 557 " ideal model delta sigma weight residual 122.79 125.69 -2.90 1.14e+00 7.69e-01 6.47e+00 ... (remaining 12623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4863 17.31 - 34.62: 440 34.62 - 51.92: 102 51.92 - 69.23: 44 69.23 - 86.54: 11 Dihedral angle restraints: 5460 sinusoidal: 2403 harmonic: 3057 Sorted by residual: dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 153.97 26.03 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CB GLU A 254 " pdb=" CG GLU A 254 " pdb=" CD GLU A 254 " pdb=" OE1 GLU A 254 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 882 0.029 - 0.058: 396 0.058 - 0.087: 121 0.087 - 0.115: 53 0.115 - 0.144: 6 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CB ILE A 494 " pdb=" CA ILE A 494 " pdb=" CG1 ILE A 494 " pdb=" CG2 ILE A 494 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ASP A 608 " pdb=" N ASP A 608 " pdb=" C ASP A 608 " pdb=" CB ASP A 608 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ASP A 336 " pdb=" N ASP A 336 " pdb=" C ASP A 336 " pdb=" CB ASP A 336 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1455 not shown) Planarity restraints: 1481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.77e+00 pdb=" C LEU A 758 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 243 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 607 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C SER A 607 " -0.022 2.00e-02 2.50e+03 pdb=" O SER A 607 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 608 " 0.008 2.00e-02 2.50e+03 ... (remaining 1478 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 223 2.67 - 3.23: 8919 3.23 - 3.79: 14895 3.79 - 4.34: 20712 4.34 - 4.90: 32504 Nonbonded interactions: 77253 Sorted by model distance: nonbonded pdb=" OD1 ASP A 761 " pdb="MG MG A1003 " model vdw 2.114 2.170 nonbonded pdb=" O ILE A 837 " pdb=" OH TYR A 884 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR A 122 " pdb=" OE1 GLU A 144 " model vdw 2.235 2.440 nonbonded pdb=" OG1 THR A 226 " pdb=" OG SER A 229 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASP A 623 " pdb=" OG SER A 682 " model vdw 2.266 2.440 ... (remaining 77248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.430 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: 3.780 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 32.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.304 9176 Z= 0.453 Angle : 0.515 5.654 12628 Z= 0.287 Chirality : 0.039 0.144 1458 Planarity : 0.003 0.033 1481 Dihedral : 14.996 86.538 3484 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.01 % Allowed : 12.05 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.22), residues: 1017 helix: -1.62 (0.20), residues: 461 sheet: -2.54 (0.52), residues: 63 loop : -2.41 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 617 HIS 0.005 0.001 HIS A 613 PHE 0.011 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.002 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7103 (tp30) REVERT: A 411 LYS cc_start: 0.7436 (mppt) cc_final: 0.7091 (mttm) REVERT: A 624 ARG cc_start: 0.8129 (mmt180) cc_final: 0.7838 (mmt180) REVERT: A 626 MET cc_start: 0.8004 (ttt) cc_final: 0.7803 (ttt) REVERT: A 826 TYR cc_start: 0.7331 (m-10) cc_final: 0.7115 (m-80) REVERT: A 924 MET cc_start: 0.7535 (mmt) cc_final: 0.7236 (mmt) REVERT: A 928 HIS cc_start: 0.6340 (OUTLIER) cc_final: 0.5755 (t70) REVERT: C 31 GLN cc_start: 0.6623 (tp-100) cc_final: 0.6421 (tp-100) REVERT: C 34 GLN cc_start: 0.8519 (tp40) cc_final: 0.8055 (tp40) outliers start: 9 outliers final: 6 residues processed: 222 average time/residue: 0.2056 time to fit residues: 63.1127 Evaluate side-chains 186 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 168 ASN A 492 GLN A 611 ASN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS B 157 GLN D 100 ASN D 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9176 Z= 0.351 Angle : 0.584 9.023 12628 Z= 0.301 Chirality : 0.042 0.257 1458 Planarity : 0.004 0.028 1481 Dihedral : 12.976 73.139 1648 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.94 % Allowed : 16.89 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.24), residues: 1017 helix: -0.90 (0.22), residues: 466 sheet: -2.31 (0.48), residues: 77 loop : -1.98 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 617 HIS 0.007 0.001 HIS C 36 PHE 0.012 0.002 PHE A 766 TYR 0.022 0.002 TYR A 788 ARG 0.003 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7194 (tp30) REVERT: A 366 LEU cc_start: 0.2231 (OUTLIER) cc_final: 0.1417 (mt) REVERT: A 411 LYS cc_start: 0.7386 (mppt) cc_final: 0.7024 (mttm) REVERT: A 463 MET cc_start: 0.7704 (ttt) cc_final: 0.7500 (ttt) REVERT: A 624 ARG cc_start: 0.8138 (mmt180) cc_final: 0.7704 (mmt180) REVERT: A 811 GLU cc_start: 0.7041 (tt0) cc_final: 0.6795 (tt0) REVERT: A 826 TYR cc_start: 0.7390 (m-10) cc_final: 0.7171 (m-80) REVERT: A 889 ARG cc_start: 0.6394 (mmt90) cc_final: 0.5859 (mmm-85) REVERT: A 924 MET cc_start: 0.7567 (mmt) cc_final: 0.7272 (mmt) REVERT: A 928 HIS cc_start: 0.6447 (OUTLIER) cc_final: 0.6058 (t70) REVERT: C 34 GLN cc_start: 0.8569 (tp40) cc_final: 0.8115 (tp40) outliers start: 35 outliers final: 23 residues processed: 216 average time/residue: 0.2019 time to fit residues: 61.2982 Evaluate side-chains 208 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9176 Z= 0.307 Angle : 0.569 9.324 12628 Z= 0.292 Chirality : 0.041 0.251 1458 Planarity : 0.003 0.028 1481 Dihedral : 12.891 73.170 1643 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.50 % Allowed : 17.57 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.24), residues: 1017 helix: -0.55 (0.23), residues: 463 sheet: -2.01 (0.51), residues: 77 loop : -1.79 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 29 HIS 0.007 0.001 HIS C 36 PHE 0.024 0.002 PHE A 157 TYR 0.019 0.001 TYR A 788 ARG 0.002 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 0.910 Fit side-chains REVERT: A 180 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7099 (tp30) REVERT: A 411 LYS cc_start: 0.7234 (mppt) cc_final: 0.6930 (mttm) REVERT: A 426 LYS cc_start: 0.8331 (mttp) cc_final: 0.7982 (mtpp) REVERT: A 483 TYR cc_start: 0.8401 (m-80) cc_final: 0.8170 (m-80) REVERT: A 758 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7682 (tp) REVERT: A 786 LEU cc_start: 0.8562 (mt) cc_final: 0.8355 (mp) REVERT: A 811 GLU cc_start: 0.6967 (tt0) cc_final: 0.6709 (tt0) REVERT: A 889 ARG cc_start: 0.6363 (mmt90) cc_final: 0.5839 (mmm-85) REVERT: A 924 MET cc_start: 0.7521 (mmt) cc_final: 0.7214 (mmt) REVERT: A 928 HIS cc_start: 0.6459 (OUTLIER) cc_final: 0.6027 (t70) REVERT: C 34 GLN cc_start: 0.8518 (tp40) cc_final: 0.8216 (tp40) outliers start: 40 outliers final: 32 residues processed: 214 average time/residue: 0.1922 time to fit residues: 58.3211 Evaluate side-chains 208 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 174 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9176 Z= 0.177 Angle : 0.512 6.703 12628 Z= 0.261 Chirality : 0.039 0.299 1458 Planarity : 0.003 0.025 1481 Dihedral : 12.788 73.202 1643 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.49 % Allowed : 20.61 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1017 helix: -0.22 (0.24), residues: 463 sheet: -1.74 (0.53), residues: 77 loop : -1.48 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 29 HIS 0.008 0.001 HIS C 36 PHE 0.014 0.001 PHE A 157 TYR 0.013 0.001 TYR A 877 ARG 0.002 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 0.907 Fit side-chains REVERT: A 180 GLU cc_start: 0.7682 (mm-30) cc_final: 0.6919 (tp30) REVERT: A 411 LYS cc_start: 0.7177 (mppt) cc_final: 0.6895 (mttm) REVERT: A 426 LYS cc_start: 0.8249 (mttp) cc_final: 0.7992 (mtpp) REVERT: A 624 ARG cc_start: 0.8055 (mmt180) cc_final: 0.7478 (mmt180) REVERT: A 787 TYR cc_start: 0.7844 (t80) cc_final: 0.7635 (t80) REVERT: A 811 GLU cc_start: 0.6977 (tt0) cc_final: 0.6690 (tt0) REVERT: A 889 ARG cc_start: 0.6300 (mmt90) cc_final: 0.5628 (mmm-85) REVERT: A 928 HIS cc_start: 0.6285 (OUTLIER) cc_final: 0.5863 (t70) REVERT: B 155 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6879 (pp20) outliers start: 31 outliers final: 20 residues processed: 216 average time/residue: 0.1923 time to fit residues: 58.4400 Evaluate side-chains 204 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 HIS B 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 9176 Z= 0.422 Angle : 0.634 6.531 12628 Z= 0.326 Chirality : 0.044 0.239 1458 Planarity : 0.004 0.030 1481 Dihedral : 12.913 73.142 1643 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.86 % Allowed : 20.27 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1017 helix: -0.35 (0.24), residues: 462 sheet: -1.86 (0.53), residues: 77 loop : -1.64 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 29 HIS 0.008 0.001 HIS A 613 PHE 0.023 0.002 PHE A 694 TYR 0.024 0.002 TYR A 788 ARG 0.003 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 181 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 180 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7508 (tp30) REVERT: A 411 LYS cc_start: 0.7173 (mppt) cc_final: 0.6894 (mttm) REVERT: A 426 LYS cc_start: 0.8355 (mttp) cc_final: 0.8028 (mtpp) REVERT: A 811 GLU cc_start: 0.7041 (tt0) cc_final: 0.6796 (tt0) REVERT: A 889 ARG cc_start: 0.6447 (mmt90) cc_final: 0.5910 (mmm-85) REVERT: A 928 HIS cc_start: 0.6435 (OUTLIER) cc_final: 0.5921 (t70) REVERT: B 139 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7739 (ttpt) REVERT: B 155 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7159 (pp20) outliers start: 52 outliers final: 45 residues processed: 216 average time/residue: 0.1857 time to fit residues: 57.6663 Evaluate side-chains 220 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 173 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 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 492 GLN ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9176 Z= 0.236 Angle : 0.549 10.296 12628 Z= 0.283 Chirality : 0.040 0.241 1458 Planarity : 0.003 0.025 1481 Dihedral : 12.862 73.151 1643 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.39 % Allowed : 22.41 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1017 helix: -0.12 (0.24), residues: 463 sheet: -1.76 (0.54), residues: 77 loop : -1.42 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 29 HIS 0.009 0.001 HIS C 36 PHE 0.012 0.001 PHE A 694 TYR 0.016 0.002 TYR A 788 ARG 0.002 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 0.926 Fit side-chains REVERT: A 180 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7341 (tp30) REVERT: A 331 ARG cc_start: 0.7017 (mtp85) cc_final: 0.6602 (ptp-170) REVERT: A 463 MET cc_start: 0.7644 (ttt) cc_final: 0.7401 (tmt) REVERT: A 499 ASP cc_start: 0.7633 (t0) cc_final: 0.7383 (t0) REVERT: A 624 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7556 (mmt180) REVERT: A 633 MET cc_start: 0.8024 (ttp) cc_final: 0.7022 (ttp) REVERT: A 787 TYR cc_start: 0.7839 (t80) cc_final: 0.7591 (t80) REVERT: A 811 GLU cc_start: 0.6964 (tt0) cc_final: 0.6683 (tt0) REVERT: A 889 ARG cc_start: 0.6350 (mmt90) cc_final: 0.5798 (mmm-85) REVERT: A 928 HIS cc_start: 0.6385 (OUTLIER) cc_final: 0.5892 (t70) REVERT: B 155 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7018 (pp20) outliers start: 39 outliers final: 32 residues processed: 212 average time/residue: 0.2016 time to fit residues: 60.4239 Evaluate side-chains 209 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9176 Z= 0.209 Angle : 0.550 10.493 12628 Z= 0.280 Chirality : 0.040 0.331 1458 Planarity : 0.003 0.024 1481 Dihedral : 12.817 73.184 1643 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.50 % Allowed : 23.65 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1017 helix: 0.02 (0.24), residues: 462 sheet: -1.87 (0.54), residues: 77 loop : -1.24 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 29 HIS 0.011 0.001 HIS C 36 PHE 0.011 0.001 PHE A 741 TYR 0.014 0.001 TYR A 831 ARG 0.002 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8350 (p) cc_final: 0.7924 (t) REVERT: A 180 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7277 (tp30) REVERT: A 331 ARG cc_start: 0.6985 (mtp85) cc_final: 0.6551 (ptp-170) REVERT: A 499 ASP cc_start: 0.7483 (t0) cc_final: 0.7235 (t0) REVERT: A 633 MET cc_start: 0.8036 (ttp) cc_final: 0.7225 (ttp) REVERT: A 811 GLU cc_start: 0.6971 (tt0) cc_final: 0.6677 (tt0) REVERT: A 889 ARG cc_start: 0.6284 (mmt90) cc_final: 0.5748 (mmm-85) REVERT: A 928 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5830 (t70) REVERT: B 94 MET cc_start: 0.5709 (ptm) cc_final: 0.4779 (ptp) REVERT: B 155 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6936 (pp20) REVERT: C 34 GLN cc_start: 0.8332 (tp40) cc_final: 0.8073 (tp40) outliers start: 40 outliers final: 34 residues processed: 203 average time/residue: 0.1993 time to fit residues: 56.8657 Evaluate side-chains 214 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 178 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9176 Z= 0.224 Angle : 0.555 10.335 12628 Z= 0.284 Chirality : 0.040 0.300 1458 Planarity : 0.003 0.025 1481 Dihedral : 12.813 73.211 1643 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.29 % Allowed : 23.42 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.26), residues: 1017 helix: 0.07 (0.24), residues: 460 sheet: -1.56 (0.58), residues: 67 loop : -1.25 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 29 HIS 0.010 0.001 HIS C 36 PHE 0.012 0.001 PHE A 694 TYR 0.015 0.001 TYR A 788 ARG 0.002 0.000 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8336 (p) cc_final: 0.7923 (t) REVERT: A 180 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7362 (tp30) REVERT: A 331 ARG cc_start: 0.7013 (mtp85) cc_final: 0.6554 (ptp-170) REVERT: A 499 ASP cc_start: 0.7429 (t0) cc_final: 0.7218 (t0) REVERT: A 633 MET cc_start: 0.8001 (ttp) cc_final: 0.7216 (ttp) REVERT: A 811 GLU cc_start: 0.6930 (tt0) cc_final: 0.6660 (tt0) REVERT: A 889 ARG cc_start: 0.6295 (mmt90) cc_final: 0.5646 (mmm-85) REVERT: A 928 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.5808 (t70) REVERT: B 94 MET cc_start: 0.5726 (ptm) cc_final: 0.4867 (ptp) REVERT: B 155 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: C 34 GLN cc_start: 0.8260 (tp40) cc_final: 0.7991 (tp40) outliers start: 47 outliers final: 36 residues processed: 210 average time/residue: 0.1969 time to fit residues: 58.6161 Evaluate side-chains 211 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9176 Z= 0.271 Angle : 0.600 10.690 12628 Z= 0.305 Chirality : 0.041 0.258 1458 Planarity : 0.003 0.025 1481 Dihedral : 12.835 73.192 1643 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.07 % Allowed : 23.42 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1017 helix: 0.03 (0.24), residues: 460 sheet: -1.89 (0.54), residues: 77 loop : -1.23 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 29 HIS 0.011 0.001 HIS C 36 PHE 0.020 0.002 PHE A 165 TYR 0.019 0.002 TYR A 787 ARG 0.003 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 0.877 Fit side-chains REVERT: A 42 VAL cc_start: 0.8368 (p) cc_final: 0.7944 (t) REVERT: A 180 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7503 (tp30) REVERT: A 331 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6623 (ptp-170) REVERT: A 499 ASP cc_start: 0.7561 (t0) cc_final: 0.7304 (t0) REVERT: A 633 MET cc_start: 0.8049 (ttp) cc_final: 0.7211 (ttp) REVERT: A 811 GLU cc_start: 0.6970 (tt0) cc_final: 0.6707 (tt0) REVERT: A 889 ARG cc_start: 0.6347 (mmt90) cc_final: 0.5691 (mmm-85) REVERT: A 928 HIS cc_start: 0.6287 (OUTLIER) cc_final: 0.5811 (t70) REVERT: B 155 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: C 34 GLN cc_start: 0.8248 (tp40) cc_final: 0.7958 (tp40) REVERT: C 55 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8310 (tt) outliers start: 45 outliers final: 38 residues processed: 204 average time/residue: 0.1916 time to fit residues: 55.3483 Evaluate side-chains 215 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9176 Z= 0.218 Angle : 0.592 9.761 12628 Z= 0.299 Chirality : 0.041 0.280 1458 Planarity : 0.003 0.025 1481 Dihedral : 12.827 73.223 1643 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.73 % Allowed : 24.10 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1017 helix: 0.11 (0.24), residues: 457 sheet: -1.86 (0.54), residues: 77 loop : -1.13 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 29 HIS 0.011 0.001 HIS C 36 PHE 0.016 0.001 PHE A 165 TYR 0.016 0.001 TYR A 787 ARG 0.002 0.000 ARG A 569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 181 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8357 (p) cc_final: 0.7937 (t) REVERT: A 180 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7343 (tp30) REVERT: A 331 ARG cc_start: 0.6989 (mtp85) cc_final: 0.6556 (ptp-170) REVERT: A 499 ASP cc_start: 0.7517 (t0) cc_final: 0.7311 (t0) REVERT: A 633 MET cc_start: 0.7965 (ttp) cc_final: 0.7178 (ttp) REVERT: A 811 GLU cc_start: 0.6924 (tt0) cc_final: 0.6654 (tt0) REVERT: A 889 ARG cc_start: 0.6263 (mmt90) cc_final: 0.5690 (mmm-85) REVERT: A 928 HIS cc_start: 0.6222 (OUTLIER) cc_final: 0.5729 (t70) REVERT: B 155 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6860 (pp20) outliers start: 42 outliers final: 36 residues processed: 206 average time/residue: 0.1902 time to fit residues: 55.7153 Evaluate side-chains 214 residues out of total 910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 HIS ** 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 = 0.4211 r_free = 0.4211 target = 0.172704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.135226 restraints weight = 10674.144| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.36 r_work: 0.3687 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9176 Z= 0.221 Angle : 0.589 10.104 12628 Z= 0.297 Chirality : 0.041 0.290 1458 Planarity : 0.003 0.029 1481 Dihedral : 12.815 73.231 1643 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.62 % Allowed : 23.76 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1017 helix: 0.12 (0.24), residues: 458 sheet: -1.78 (0.55), residues: 77 loop : -1.09 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 29 HIS 0.011 0.001 HIS C 36 PHE 0.014 0.001 PHE A 165 TYR 0.014 0.001 TYR A 788 ARG 0.001 0.000 ARG A 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2161.75 seconds wall clock time: 40 minutes 2.71 seconds (2402.71 seconds total)