Starting phenix.real_space_refine on Mon Oct 26 18:44:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tnz_10540/10_2026/6tnz_10540_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tnz_10540/10_2026/6tnz_10540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tnz_10540/10_2026/6tnz_10540_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tnz_10540/10_2026/6tnz_10540_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tnz_10540/10_2026/6tnz_10540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tnz_10540/10_2026/6tnz_10540.map" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 1 6.06 5 P 53 5.49 5 S 138 5.16 5 C 13762 2.51 5 N 3773 2.21 5 O 4277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22008 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 8085 Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3304 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1130 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 554 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 7, 'TRANS': 58} Chain: "E" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1924 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "H" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2282 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Unusual residues: {'DOC': 1} Classifications: {'DNA': 22, 'undetermined': 1} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres=" DG P 24 " pdbres="DOC P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' ZN': 1, 'SF4': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7157 SG CYS A1012 49.935 80.376 108.380 1.00 40.62 S ATOM 7175 SG CYS A1015 52.994 80.952 110.751 1.00 40.62 S ATOM 7248 SG CYS A1026 49.548 80.568 112.525 1.00 40.62 S ATOM 7264 SG CYS A1029 50.117 83.298 109.946 1.00 40.62 S ATOM 7616 SG CYS A1071 56.907 69.988 66.993 1.00 40.62 S ATOM 7654 SG CYS A1076 60.245 74.421 69.196 1.00 30.94 S ATOM 7515 SG CYS A1058 53.360 74.155 70.247 1.00 40.62 S ATOM 7541 SG CYS A1061 56.466 75.272 64.727 1.00 24.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A1100 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1100 " occ=0.50 Time building chain proxies: 6.30, per 1000 atoms: 0.29 Number of scatterers: 22008 At special positions: 0 Unit cell: (150.51, 153.99, 151.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 4 26.01 S 138 16.00 P 53 15.00 O 4277 8.00 N 3773 7.00 C 13762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1202 " pdb="FE1 SF4 A1202 " - pdb=" SG CYS A1071 " pdb="FE2 SF4 A1202 " - pdb=" SG CYS A1076 " pdb="FE3 SF4 A1202 " - pdb=" SG CYS A1058 " pdb="FE4 SF4 A1202 " - pdb=" SG CYS A1061 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1029 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1015 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1026 " Number of angles added : 6 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5076 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 22 sheets defined 33.1% alpha, 20.8% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.640A pdb=" N SER A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.925A pdb=" N GLU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.592A pdb=" N GLN A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.573A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 413 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 473 through 482 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 501 through 526 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 527 through 540 removed outlier: 3.590A pdb=" N ASN A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.641A pdb=" N LEU A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 548 " --> pdb=" O TYR A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 551 through 564 removed outlier: 4.128A pdb=" N VAL A 555 " --> pdb=" O GLN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 655 through 675 Processing helix chain 'A' and resid 679 through 705 removed outlier: 3.886A pdb=" N TYR A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 739 removed outlier: 3.936A pdb=" N SER A 717 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 783 Processing helix chain 'A' and resid 837 through 853 Processing helix chain 'A' and resid 856 through 873 Processing helix chain 'A' and resid 898 through 906 removed outlier: 3.629A pdb=" N GLU A 902 " --> pdb=" O GLN A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 949 Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 962 through 971 removed outlier: 3.563A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 988 Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.794A pdb=" N ALA A1004 " --> pdb=" O GLY A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1056 removed outlier: 4.885A pdb=" N GLU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A1041 " --> pdb=" O TYR A1037 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A1052 " --> pdb=" O GLU A1048 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1053 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1054 " --> pdb=" O ARG A1050 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1063 removed outlier: 3.573A pdb=" N ARG A1060 " --> pdb=" O THR A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1096 removed outlier: 3.691A pdb=" N MET A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A1084 " --> pdb=" O TYR A1080 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A1085 " --> pdb=" O MET A1081 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A1094 " --> pdb=" O GLU A1090 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A1096 " --> pdb=" O GLN A1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.600A pdb=" N ALA B 7 " --> pdb=" O GLU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 50 through 74 removed outlier: 4.281A pdb=" N TYR B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.901A pdb=" N GLN B 71 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 272 through 288 removed outlier: 3.966A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 removed outlier: 3.626A pdb=" N MET B 315 " --> pdb=" O HIS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.802A pdb=" N TYR B 322 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 355 removed outlier: 3.558A pdb=" N TYR B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.671A pdb=" N THR C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 30 removed outlier: 3.896A pdb=" N LEU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 52 removed outlier: 3.888A pdb=" N ASN C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.507A pdb=" N VAL C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.822A pdb=" N ASN C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.599A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.855A pdb=" N ARG D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 18 removed outlier: 4.177A pdb=" N LYS E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.812A pdb=" N HIS E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 217 through 222 Proline residue: E 220 - end of helix No H-bonds generated for 'chain 'E' and resid 217 through 222' Processing helix chain 'F' and resid 8 through 20 removed outlier: 4.058A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 8 through 20 removed outlier: 4.016A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.591A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 61 through 77 removed outlier: 4.389A pdb=" N MET H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR H 71 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 101 removed outlier: 4.454A pdb=" N ALA H 98 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS H 99 " --> pdb=" O GLU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 140 Processing helix chain 'H' and resid 140 through 145 removed outlier: 3.816A pdb=" N LEU H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 168 Processing helix chain 'H' and resid 180 through 185 removed outlier: 3.629A pdb=" N THR H 184 " --> pdb=" O MET H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.724A pdb=" N GLN H 214 " --> pdb=" O SER H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 232 removed outlier: 3.564A pdb=" N LEU H 226 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER H 232 " --> pdb=" O ILE H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 253 removed outlier: 3.585A pdb=" N VAL H 247 " --> pdb=" O PRO H 243 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 263 removed outlier: 3.995A pdb=" N ARG H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 283 Processing helix chain 'H' and resid 302 through 308 Processing helix chain 'H' and resid 317 through 331 removed outlier: 3.526A pdb=" N ILE H 321 " --> pdb=" O SER H 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 286 through 291 removed outlier: 6.565A pdb=" N SER A 136 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA A 288 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS A 138 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL A 290 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS A 140 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 100 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 130 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 98 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TRP A 265 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.530A pdb=" N GLN A 369 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 336 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A 311 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N THR A 394 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 313 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 393 " --> pdb=" O MET A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 438 Processing sheet with id=AA5, first strand: chain 'A' and resid 592 through 594 removed outlier: 5.416A pdb=" N PHE A 794 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP A 602 " --> pdb=" O PHE A 794 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 796 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 753 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 762 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL A 751 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.209A pdb=" N TYR A 798 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 814 " --> pdb=" O TYR A 798 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 812 " --> pdb=" O PRO A 800 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 621 through 622 removed outlier: 4.674A pdb=" N GLU A 645 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 883 through 886 Processing sheet with id=AA9, first strand: chain 'A' and resid 992 through 993 removed outlier: 3.788A pdb=" N THR A 993 " --> pdb=" O ASP F 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.652A pdb=" N GLU B 132 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 160 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 176 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 327 removed outlier: 7.701A pdb=" N PHE B 195 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 241 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 197 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU B 243 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B 199 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER C 73 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS C 75 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 79 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS C 58 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE C 103 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 60 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 99 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 97 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 103 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL C 21 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 332 through 336 removed outlier: 6.616A pdb=" N ARG B 340 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE B 403 " --> pdb=" O ARG B 340 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 342 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 426 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 411 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB5, first strand: chain 'E' and resid 66 through 71 removed outlier: 7.298A pdb=" N GLU E 25 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET E 40 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N CYS E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 123 through 125 Processing sheet with id=AB7, first strand: chain 'E' and resid 178 through 183 Processing sheet with id=AB8, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.359A pdb=" N VAL F 111 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS G 181 " --> pdb=" O VAL F 111 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP F 113 " --> pdb=" O ASN G 179 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN G 179 " --> pdb=" O ASP F 113 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN G 177 " --> pdb=" O GLU F 115 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 68 through 71 removed outlier: 7.288A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN F 36 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 178 through 183 Processing sheet with id=AC2, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.646A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 66 through 71 removed outlier: 7.094A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 18 through 21 removed outlier: 6.100A pdb=" N ALA H 175 " --> pdb=" O MET H 191 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS H 30 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ALA H 176 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA H 32 " --> pdb=" O ALA H 176 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 8934 1.40 - 1.63: 13377 1.63 - 1.85: 209 1.85 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 22532 Sorted by residual: bond pdb=" C2' TTP A1203 " pdb=" C3' TTP A1203 " ideal model delta sigma weight residual 1.522 1.216 0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C3' DOC P 25 " pdb=" C2' DOC P 25 " ideal model delta sigma weight residual 1.521 1.306 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C4' TTP A1203 " pdb=" O4' TTP A1203 " ideal model delta sigma weight residual 1.426 1.270 0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" C4' DOC P 25 " pdb=" O4' DOC P 25 " ideal model delta sigma weight residual 1.431 1.278 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" O4' DOC P 25 " pdb=" C1' DOC P 25 " ideal model delta sigma weight residual 1.405 1.551 -0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 22527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 29804 2.86 - 5.71: 797 5.71 - 8.57: 127 8.57 - 11.43: 17 11.43 - 14.28: 5 Bond angle restraints: 30750 Sorted by residual: angle pdb=" N ALA B 179 " pdb=" CA ALA B 179 " pdb=" C ALA B 179 " ideal model delta sigma weight residual 111.28 119.43 -8.15 1.09e+00 8.42e-01 5.58e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.74 7.62 1.09e+00 8.42e-01 4.89e+01 angle pdb=" N ILE H 241 " pdb=" CA ILE H 241 " pdb=" C ILE H 241 " ideal model delta sigma weight residual 109.51 119.40 -9.89 1.43e+00 4.89e-01 4.78e+01 angle pdb=" N GLY A 592 " pdb=" CA GLY A 592 " pdb=" C GLY A 592 " ideal model delta sigma weight residual 110.20 118.98 -8.78 1.32e+00 5.74e-01 4.43e+01 angle pdb=" N ALA A1024 " pdb=" CA ALA A1024 " pdb=" C ALA A1024 " ideal model delta sigma weight residual 111.28 118.45 -7.17 1.09e+00 8.42e-01 4.32e+01 ... (remaining 30745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.43: 12060 20.43 - 40.86: 1191 40.86 - 61.30: 330 61.30 - 81.73: 34 81.73 - 102.16: 16 Dihedral angle restraints: 13631 sinusoidal: 5785 harmonic: 7846 Sorted by residual: dihedral pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CA HIS A1021 " pdb=" CB HIS A1021 " ideal model delta harmonic sigma weight residual 122.80 137.58 -14.78 0 2.50e+00 1.60e-01 3.50e+01 dihedral pdb=" CA PRO A 818 " pdb=" C PRO A 818 " pdb=" N ASP A 819 " pdb=" CA ASP A 819 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LEU A 962 " pdb=" C LEU A 962 " pdb=" N ALA A 963 " pdb=" CA ALA A 963 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 13628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3068 0.098 - 0.196: 404 0.196 - 0.295: 31 0.295 - 0.393: 2 0.393 - 0.491: 4 Chirality restraints: 3509 Sorted by residual: chirality pdb=" CA ASP B 180 " pdb=" N ASP B 180 " pdb=" C ASP B 180 " pdb=" CB ASP B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA HIS A1021 " pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CB HIS A1021 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB ILE A1078 " pdb=" CA ILE A1078 " pdb=" CG1 ILE A1078 " pdb=" CG2 ILE A1078 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 3506 not shown) Planarity restraints: 3799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C PHE A1099 " -0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " 0.029 2.00e-02 2.50e+03 pdb=" N AGLY A1100 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C PHE A1099 " -0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " 0.029 2.00e-02 2.50e+03 pdb=" N BGLY A1100 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 173 " -0.058 2.00e-02 2.50e+03 3.20e-02 2.05e+01 pdb=" CG TYR H 173 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR H 173 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR H 173 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR H 173 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR H 173 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 173 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR H 173 " -0.052 2.00e-02 2.50e+03 ... (remaining 3796 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 137 2.52 - 3.11: 14645 3.11 - 3.71: 32303 3.71 - 4.30: 45680 4.30 - 4.90: 75559 Nonbonded interactions: 168324 Sorted by model distance: nonbonded pdb=" O ASP E 232 " pdb=" CE1 PHE H 343 " model vdw 1.921 3.340 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 1.985 3.860 nonbonded pdb=" SG CYS E 27 " pdb=" CG LEU H 350 " model vdw 2.016 3.830 nonbonded pdb=" N LEU E 121 " pdb=" OG SER H 352 " model vdw 2.056 3.120 nonbonded pdb=" CD PRO E 129 " pdb=" CD1 PHE H 344 " model vdw 2.060 3.740 ... (remaining 168319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 1 through 107 or resid 109 through 185 or resid 191 or res \ id 194 through 255)) selection = (chain 'F' and (resid 1 through 191 or resid 194 through 255)) selection = (chain 'G' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 185 or resid 193 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 29.150 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 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 : 0.009 0.306 22541 Z= 0.464 Angle : 1.216 39.373 30768 Z= 0.702 Chirality : 0.067 0.491 3509 Planarity : 0.008 0.075 3799 Dihedral : 17.568 102.161 8555 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.84 % Favored : 91.08 % Rotamer: Outliers : 1.57 % Allowed : 8.95 % Favored : 89.48 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.14), residues: 2670 helix: -2.76 (0.14), residues: 799 sheet: -1.00 (0.20), residues: 630 loop : -3.12 (0.14), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 276 TYR 0.058 0.004 TYR H 173 PHE 0.032 0.004 PHE A 637 TRP 0.037 0.004 TRP A 344 HIS 0.011 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.46 (22532) covalent geometry : angle 1.16764 / 0.70 (30750) hydrogen bonds : bond 0.15899 / 11.05 ( 929) hydrogen bonds : angle 7.43635 / 5.21 ( 2564) metal coordination : bond 0.12635 / 6.20 ( 8) metal coordination : angle 14.03078 / 7.94 ( 18) Misc. bond : bond 0.00591 / 0.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 364 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ASP cc_start: 0.8275 (m-30) cc_final: 0.8001 (m-30) REVERT: E 35 VAL cc_start: 0.6311 (t) cc_final: 0.5579 (t) REVERT: E 47 LEU cc_start: 0.8010 (tt) cc_final: 0.7443 (mt) outliers start: 36 outliers final: 6 residues processed: 393 average time/residue: 0.1727 time to fit residues: 101.2241 Evaluate side-chains 174 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS A 558 GLN A 726 GLN A 842 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 HIS A 955 GLN ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN A1066 HIS A1092 GLN B 21 ASN B 70 GLN B 285 GLN C 58 HIS C 116 ASN D 91 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN G 49 GLN G 108 GLN G 153 HIS G 204 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN H 77 ASN H 222 GLN H 253 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.073747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.055757 restraints weight = 143534.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.057028 restraints weight = 92799.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.057261 restraints weight = 57593.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.057638 restraints weight = 43682.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.057761 restraints weight = 36946.052| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22541 Z= 0.239 Angle : 0.883 27.967 30768 Z= 0.439 Chirality : 0.049 0.274 3509 Planarity : 0.007 0.063 3799 Dihedral : 14.896 92.109 3517 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.96 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.15), residues: 2670 helix: -1.10 (0.17), residues: 806 sheet: -0.48 (0.20), residues: 626 loop : -2.62 (0.15), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 443 TYR 0.032 0.003 TYR H 26 PHE 0.035 0.003 PHE H 27 TRP 0.049 0.003 TRP H 274 HIS 0.008 0.002 HIS H 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 (22532) covalent geometry : angle 0.84349 / 0.44 (30750) hydrogen bonds : bond 0.05469 / 3.57 ( 929) hydrogen bonds : angle 5.74168 / 4.03 ( 2564) metal coordination : bond 0.02203 / 0.86 ( 8) metal coordination : angle 10.81981 / 5.88 ( 18) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.8642 (mtm) cc_final: 0.7899 (mmm) REVERT: E 229 MET cc_start: 0.4311 (mpp) cc_final: 0.3332 (ttp) REVERT: E 249 TYR cc_start: 0.8702 (m-10) cc_final: 0.8458 (m-80) REVERT: F 139 MET cc_start: 0.7918 (tmm) cc_final: 0.7681 (tmm) REVERT: G 119 MET cc_start: 0.5588 (mpp) cc_final: 0.5344 (mpp) REVERT: H 65 MET cc_start: 0.4784 (tpt) cc_final: 0.4188 (mtt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1540 time to fit residues: 47.9602 Evaluate side-chains 127 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [258, 138, 118, 103, 88, 206, 156, 179, 16, 260, 73] chunk 258 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 260 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 GLN B 184 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.070324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.052316 restraints weight = 146545.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.052829 restraints weight = 107492.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053290 restraints weight = 66954.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.053148 restraints weight = 61449.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.053207 restraints weight = 50883.847| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 22541 Z= 0.300 Angle : 0.930 34.146 30768 Z= 0.453 Chirality : 0.051 0.203 3509 Planarity : 0.007 0.060 3799 Dihedral : 14.884 96.918 3517 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.71 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 2670 helix: -0.61 (0.18), residues: 807 sheet: -0.62 (0.19), residues: 654 loop : -2.68 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 224 TYR 0.043 0.003 TYR H 26 PHE 0.031 0.003 PHE A 156 TRP 0.028 0.002 TRP A 79 HIS 0.013 0.002 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.30 (22532) covalent geometry : angle 0.87023 / 0.45 (30750) hydrogen bonds : bond 0.05782 / 3.83 ( 929) hydrogen bonds : angle 5.64864 / 3.97 ( 2564) metal coordination : bond 0.01776 / 0.67 ( 8) metal coordination : angle 13.61047 / 7.28 ( 18) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.8644 (mtm) cc_final: 0.8020 (mmm) REVERT: B 295 MET cc_start: 0.6841 (mtm) cc_final: 0.6635 (mtp) REVERT: E 196 THR cc_start: 0.8068 (m) cc_final: 0.7801 (p) REVERT: F 139 MET cc_start: 0.8176 (tmm) cc_final: 0.7862 (tmm) REVERT: G 119 MET cc_start: 0.5694 (mpp) cc_final: 0.5341 (mpp) REVERT: H 191 MET cc_start: 0.0163 (ttt) cc_final: -0.0056 (ttt) outliers start: 4 outliers final: 1 residues processed: 166 average time/residue: 0.1397 time to fit residues: 38.5589 Evaluate side-chains 123 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [198, 186, 50, 79, 246, 75, 221, 207, 224, 208, 233] chunk 198 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 246 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 233 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.070871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.050322 restraints weight = 145907.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.051468 restraints weight = 85643.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.052197 restraints weight = 59275.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052747 restraints weight = 46041.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.053064 restraints weight = 38664.085| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22541 Z= 0.188 Angle : 0.770 29.818 30768 Z= 0.372 Chirality : 0.047 0.258 3509 Planarity : 0.005 0.051 3799 Dihedral : 14.453 96.201 3517 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.15), residues: 2670 helix: -0.16 (0.18), residues: 812 sheet: -0.47 (0.19), residues: 658 loop : -2.43 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 232 TYR 0.021 0.002 TYR H 173 PHE 0.014 0.002 PHE A 420 TRP 0.025 0.002 TRP D 56 HIS 0.006 0.001 HIS H 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (22532) covalent geometry : angle 0.71388 / 0.37 (30750) hydrogen bonds : bond 0.04659 / 3.07 ( 929) hydrogen bonds : angle 5.28467 / 3.71 ( 2564) metal coordination : bond 0.01966 / 1.17 ( 8) metal coordination : angle 11.97379 / 6.33 ( 18) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8437 (mtp) cc_final: 0.8144 (mmm) REVERT: A 727 MET cc_start: 0.8731 (mtm) cc_final: 0.8031 (mmm) REVERT: E 196 THR cc_start: 0.7853 (m) cc_final: 0.7599 (t) REVERT: E 229 MET cc_start: 0.5007 (mpp) cc_final: 0.4367 (mpp) REVERT: E 235 LEU cc_start: 0.8372 (tp) cc_final: 0.8135 (tp) REVERT: G 1 MET cc_start: 0.5702 (ttt) cc_final: 0.5484 (ttp) REVERT: G 75 MET cc_start: 0.8956 (mtp) cc_final: 0.8622 (mtm) REVERT: G 119 MET cc_start: 0.5272 (mpp) cc_final: 0.5033 (mpp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1400 time to fit residues: 36.3606 Evaluate side-chains 124 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [142, 47, 73, 198, 57, 209, 123, 7, 115, 157, 237] chunk 142 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 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 = 0.3845 r_free = 0.3845 target = 0.071011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.052592 restraints weight = 143989.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.053229 restraints weight = 88410.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.053404 restraints weight = 58083.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.053706 restraints weight = 44015.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.053954 restraints weight = 36984.682| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22541 Z= 0.149 Angle : 0.735 38.757 30768 Z= 0.347 Chirality : 0.045 0.200 3509 Planarity : 0.005 0.048 3799 Dihedral : 14.231 97.168 3517 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2670 helix: 0.26 (0.18), residues: 807 sheet: -0.32 (0.20), residues: 654 loop : -2.27 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 53 TYR 0.022 0.002 TYR A 244 PHE 0.013 0.001 PHE F 144 TRP 0.017 0.001 TRP D 56 HIS 0.005 0.001 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (22532) covalent geometry : angle 0.66178 / 0.35 (30750) hydrogen bonds : bond 0.04322 / 2.85 ( 929) hydrogen bonds : angle 5.11703 / 3.60 ( 2564) metal coordination : bond 0.02341 / 1.50 ( 8) metal coordination : angle 13.25250 / 7.66 ( 18) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8331 (mtp) cc_final: 0.8064 (mmm) REVERT: A 727 MET cc_start: 0.8661 (mtm) cc_final: 0.8003 (mmm) REVERT: B 81 LYS cc_start: 0.8037 (tptt) cc_final: 0.7530 (mmtm) REVERT: B 351 ASP cc_start: 0.7792 (t70) cc_final: 0.7557 (t70) REVERT: E 119 MET cc_start: 0.2690 (pmm) cc_final: 0.2405 (pmm) REVERT: E 196 THR cc_start: 0.7862 (m) cc_final: 0.7595 (t) REVERT: E 229 MET cc_start: 0.4790 (mpp) cc_final: 0.4180 (mpp) REVERT: G 119 MET cc_start: 0.5206 (mpp) cc_final: 0.4991 (mpp) REVERT: H 6 LEU cc_start: 0.5215 (tp) cc_final: 0.4532 (tp) REVERT: H 67 MET cc_start: -0.0432 (tpp) cc_final: -0.1153 (tpt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1432 time to fit residues: 36.7236 Evaluate side-chains 124 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [211, 151, 24, 88, 178, 107, 44, 11, 93, 269, 212] chunk 211 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 0.1980 chunk 269 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.070045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.051641 restraints weight = 147110.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.052167 restraints weight = 91738.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.052500 restraints weight = 58967.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.052747 restraints weight = 44503.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052921 restraints weight = 38979.993| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22541 Z= 0.183 Angle : 0.763 40.381 30768 Z= 0.361 Chirality : 0.046 0.198 3509 Planarity : 0.005 0.052 3799 Dihedral : 14.251 98.624 3517 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2670 helix: 0.32 (0.18), residues: 807 sheet: -0.31 (0.19), residues: 654 loop : -2.24 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 990 TYR 0.021 0.002 TYR A 244 PHE 0.015 0.002 PHE A 418 TRP 0.045 0.002 TRP H 274 HIS 0.006 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (22532) covalent geometry : angle 0.69428 / 0.36 (30750) hydrogen bonds : bond 0.04455 / 2.91 ( 929) hydrogen bonds : angle 5.13339 / 3.61 ( 2564) metal coordination : bond 0.02707 / 1.88 ( 8) metal coordination : angle 13.13094 / 7.38 ( 18) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 629 LYS cc_start: 0.8078 (tppt) cc_final: 0.7561 (tptp) REVERT: A 727 MET cc_start: 0.8659 (mtm) cc_final: 0.8076 (mmm) REVERT: B 81 LYS cc_start: 0.8045 (tptt) cc_final: 0.7519 (mmtm) REVERT: E 229 MET cc_start: 0.4646 (mpp) cc_final: 0.4186 (mpp) REVERT: H 67 MET cc_start: -0.0541 (tpp) cc_final: -0.1166 (tpt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1370 time to fit residues: 33.4527 Evaluate side-chains 118 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [116, 200, 219, 15, 168, 180, 260, 264, 10, 34, 97] chunk 116 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 chunk 180 optimal weight: 30.0000 chunk 260 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 HIS B 225 GLN ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.068694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.050535 restraints weight = 147989.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.050902 restraints weight = 94796.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.050961 restraints weight = 63040.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.051400 restraints weight = 50351.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.051655 restraints weight = 40705.940| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 22541 Z= 0.237 Angle : 0.843 43.608 30768 Z= 0.397 Chirality : 0.048 0.225 3509 Planarity : 0.005 0.054 3799 Dihedral : 14.375 101.390 3517 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.27 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.16), residues: 2670 helix: 0.08 (0.18), residues: 822 sheet: -0.53 (0.19), residues: 643 loop : -2.32 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 232 TYR 0.023 0.002 TYR A 244 PHE 0.022 0.002 PHE A1099 TRP 0.022 0.002 TRP D 56 HIS 0.008 0.002 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 (22532) covalent geometry : angle 0.77045 / 0.40 (30750) hydrogen bonds : bond 0.04951 / 3.24 ( 929) hydrogen bonds : angle 5.32638 / 3.75 ( 2564) metal coordination : bond 0.02638 / 1.71 ( 8) metal coordination : angle 14.19045 / 7.68 ( 18) Misc. bond : bond 0.00047 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.792 Fit side-chains REVERT: A 160 HIS cc_start: 0.9309 (m90) cc_final: 0.9065 (m90) REVERT: A 255 MET cc_start: 0.8184 (mtt) cc_final: 0.7699 (mmm) REVERT: A 629 LYS cc_start: 0.8131 (tppt) cc_final: 0.7770 (tptm) REVERT: A 727 MET cc_start: 0.8605 (mtm) cc_final: 0.8090 (mmm) REVERT: B 81 LYS cc_start: 0.8147 (tptt) cc_final: 0.7611 (mmtp) REVERT: E 229 MET cc_start: 0.4769 (mpp) cc_final: 0.4452 (mpp) REVERT: E 250 TYR cc_start: 0.8038 (m-80) cc_final: 0.7824 (m-80) REVERT: G 75 MET cc_start: 0.8340 (mpp) cc_final: 0.7982 (mpp) REVERT: G 119 MET cc_start: 0.6029 (mpp) cc_final: 0.5719 (mpp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1293 time to fit residues: 29.7828 Evaluate side-chains 113 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [92, 135, 38, 149, 100, 66, 75, 69, 4, 199, 27] chunk 92 optimal weight: 0.1980 chunk 135 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 100 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN F 44 HIS ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN G 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.070621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.052405 restraints weight = 144921.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.052737 restraints weight = 88671.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052925 restraints weight = 59764.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.053243 restraints weight = 49189.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.053575 restraints weight = 38764.264| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22541 Z= 0.120 Angle : 0.704 32.607 30768 Z= 0.334 Chirality : 0.045 0.258 3509 Planarity : 0.005 0.052 3799 Dihedral : 14.055 99.633 3517 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.46 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.16), residues: 2670 helix: 0.68 (0.19), residues: 801 sheet: -0.29 (0.20), residues: 632 loop : -2.05 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 240 TYR 0.019 0.001 TYR A 244 PHE 0.013 0.001 PHE C 13 TRP 0.017 0.002 TRP A1055 HIS 0.010 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (22532) covalent geometry : angle 0.64556 / 0.33 (30750) hydrogen bonds : bond 0.03909 / 2.59 ( 929) hydrogen bonds : angle 4.89645 / 3.45 ( 2564) metal coordination : bond 0.01626 / 1.15 ( 8) metal coordination : angle 11.60519 / 7.04 ( 18) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.836 Fit side-chains REVERT: A 255 MET cc_start: 0.8310 (mtt) cc_final: 0.8033 (mtp) REVERT: A 629 LYS cc_start: 0.8124 (tppt) cc_final: 0.7721 (tptp) REVERT: A 727 MET cc_start: 0.8569 (mtm) cc_final: 0.8069 (mmm) REVERT: A 937 MET cc_start: 0.7640 (mmm) cc_final: 0.7439 (mmm) REVERT: B 81 LYS cc_start: 0.8025 (tptt) cc_final: 0.7468 (mmtm) REVERT: B 278 MET cc_start: 0.7785 (mpp) cc_final: 0.7562 (mtm) REVERT: E 229 MET cc_start: 0.4789 (mpp) cc_final: 0.4284 (mpp) REVERT: G 75 MET cc_start: 0.8125 (mpp) cc_final: 0.7807 (mpp) REVERT: H 180 MET cc_start: -0.2898 (ttm) cc_final: -0.3199 (ttm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1297 time to fit residues: 31.8294 Evaluate side-chains 117 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [46, 5, 54, 128, 189, 122, 41, 226, 50, 4, 53] chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 226 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN G 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.068954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.051479 restraints weight = 148397.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.052228 restraints weight = 100740.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.051909 restraints weight = 67641.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.052215 restraints weight = 52691.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.052363 restraints weight = 43304.558| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22541 Z= 0.190 Angle : 0.770 37.758 30768 Z= 0.364 Chirality : 0.046 0.277 3509 Planarity : 0.005 0.053 3799 Dihedral : 14.155 102.287 3517 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.21 % Rotamer: Outliers : 0.04 % Allowed : 0.70 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2670 helix: 0.51 (0.18), residues: 814 sheet: -0.42 (0.20), residues: 623 loop : -2.16 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 232 TYR 0.020 0.002 TYR A 244 PHE 0.018 0.002 PHE A 418 TRP 0.029 0.002 TRP E 28 HIS 0.008 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (22532) covalent geometry : angle 0.70748 / 0.36 (30750) hydrogen bonds : bond 0.04485 / 2.94 ( 929) hydrogen bonds : angle 5.03301 / 3.53 ( 2564) metal coordination : bond 0.02250 / 1.50 ( 8) metal coordination : angle 12.59097 / 7.15 ( 18) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 160 HIS cc_start: 0.9341 (m90) cc_final: 0.9100 (m90) REVERT: A 255 MET cc_start: 0.8277 (mtt) cc_final: 0.7711 (mmm) REVERT: A 629 LYS cc_start: 0.8097 (tppt) cc_final: 0.7780 (pptt) REVERT: A 727 MET cc_start: 0.8509 (mtm) cc_final: 0.7994 (mmm) REVERT: A 937 MET cc_start: 0.7613 (mmm) cc_final: 0.7390 (mmm) REVERT: B 81 LYS cc_start: 0.8104 (tptt) cc_final: 0.7609 (mmtp) REVERT: E 229 MET cc_start: 0.4714 (mpp) cc_final: 0.4450 (mpp) REVERT: E 250 TYR cc_start: 0.7969 (m-80) cc_final: 0.7750 (m-80) REVERT: F 184 GLN cc_start: 0.5884 (OUTLIER) cc_final: 0.5590 (mm-40) REVERT: G 75 MET cc_start: 0.8182 (mpp) cc_final: 0.7820 (mpp) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1346 time to fit residues: 31.1963 Evaluate side-chains 110 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [34, 184, 267, 75, 67, 187, 250, 135, 252, 149, 139] chunk 34 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 267 optimal weight: 30.0000 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 252 optimal weight: 0.2980 chunk 149 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN F 184 GLN G 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.068775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.051253 restraints weight = 149081.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.051940 restraints weight = 105835.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052240 restraints weight = 64622.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.052208 restraints weight = 61086.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.052262 restraints weight = 50014.666| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22541 Z= 0.190 Angle : 0.774 38.619 30768 Z= 0.366 Chirality : 0.046 0.207 3509 Planarity : 0.005 0.064 3799 Dihedral : 14.215 103.545 3517 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.16), residues: 2670 helix: 0.38 (0.18), residues: 820 sheet: -0.58 (0.20), residues: 629 loop : -2.20 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 232 TYR 0.016 0.002 TYR A 244 PHE 0.018 0.002 PHE A1099 TRP 0.055 0.002 TRP D 56 HIS 0.008 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (22532) covalent geometry : angle 0.70894 / 0.36 (30750) hydrogen bonds : bond 0.04488 / 2.95 ( 929) hydrogen bonds : angle 5.12237 / 3.59 ( 2564) metal coordination : bond 0.02363 / 1.53 ( 8) metal coordination : angle 12.90957 / 7.35 ( 18) Misc. bond : bond 0.00050 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5340 Ramachandran restraints generated. 2670 Oldfield, 0 Emsley, 2670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.833 Fit side-chains REVERT: A 160 HIS cc_start: 0.9299 (m90) cc_final: 0.9083 (m90) REVERT: A 255 MET cc_start: 0.8285 (mtt) cc_final: 0.7996 (mtp) REVERT: A 629 LYS cc_start: 0.8284 (tppt) cc_final: 0.7943 (pptt) REVERT: A 727 MET cc_start: 0.8494 (mtm) cc_final: 0.8011 (mmm) REVERT: A 937 MET cc_start: 0.7574 (mmm) cc_final: 0.7349 (mmm) REVERT: B 81 LYS cc_start: 0.8211 (tptt) cc_final: 0.7714 (mmtp) REVERT: E 229 MET cc_start: 0.4889 (mpp) cc_final: 0.4315 (mpp) REVERT: E 250 TYR cc_start: 0.7980 (m-80) cc_final: 0.7736 (m-80) REVERT: H 180 MET cc_start: -0.2728 (ttm) cc_final: -0.2989 (ttm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1406 time to fit residues: 32.0099 Evaluate side-chains 112 residues out of total 2339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: [200, 145, 233, 189, 20, 213, 74, 85, 158, 206, 256] chunk 200 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 20 optimal weight: 0.0060 chunk 213 optimal weight: 20.0000 chunk 74 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 overall best weight: 2.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN G 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.068796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.050737 restraints weight = 147768.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050953 restraints weight = 92880.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.051011 restraints weight = 64242.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.051403 restraints weight = 51754.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.051625 restraints weight = 41634.292| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22541 Z= 0.171 Angle : 0.757 37.339 30768 Z= 0.356 Chirality : 0.046 0.221 3509 Planarity : 0.005 0.058 3799 Dihedral : 14.159 104.002 3517 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.12 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.16), residues: 2670 helix: 0.47 (0.18), residues: 820 sheet: -0.53 (0.20), residues: 627 loop : -2.17 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 232 TYR 0.020 0.002 TYR A 244 PHE 0.016 0.002 PHE A 241 TRP 0.032 0.002 TRP D 56 HIS 0.008 0.001 HIS A1021 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (22532) covalent geometry : angle 0.69174 / 0.35 (30750) hydrogen bonds : bond 0.04350 / 2.86 ( 929) hydrogen bonds : angle 5.08084 / 3.58 ( 2564) metal coordination : bond 0.02181 / 1.46 ( 8) metal coordination : angle 12.77890 / 7.31 ( 18) Misc. bond : bond 0.00049 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4457.94 seconds wall clock time: 77 minutes 18.05 seconds (4638.05 seconds total)