Starting phenix.real_space_refine on Sat Sep 28 09:33:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/09_2024/6z2j_11041_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/09_2024/6z2j_11041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/09_2024/6z2j_11041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/09_2024/6z2j_11041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/09_2024/6z2j_11041_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z2j_11041/09_2024/6z2j_11041_trim.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 4 8.98 5 Zn 2 6.06 5 P 12 5.49 5 S 61 5.16 5 C 6096 2.51 5 N 1626 2.21 5 O 1802 1.98 5 H 9273 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18876 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 5800 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 5785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5785 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Conformer: "B" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} bond proxies already assigned to first conformer: 1060 Chain: "B" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1098 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2488 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2488 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' K': 2, ' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' K': 2, ' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ACYS A 121 " occ=0.50 ... (20 atoms not shown) pdb=" HG BCYS A 121 " occ=0.50 residue: pdb=" C1 IHP C 501 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP C 501 " occ=0.70 residue: pdb=" C1 IHP E 501 " occ=0.70 ... (34 atoms not shown) pdb=" P6 IHP E 501 " occ=0.70 Time building chain proxies: 10.71, per 1000 atoms: 0.57 Number of scatterers: 18876 At special positions: 0 Unit cell: (149.04, 166.32, 69.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 4 19.00 S 61 16.00 P 12 15.00 O 1802 8.00 N 1626 7.00 C 6096 6.00 H 9273 1.00 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: 4.80 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 178 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 178 " 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 55.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.603A pdb=" N GLY C 20 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN C 21 " --> pdb=" O ASP C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 45 removed outlier: 3.706A pdb=" N MET C 37 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 43 " --> pdb=" O HIS C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.811A pdb=" N MET C 51 " --> pdb=" O TYR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.737A pdb=" N MET C 64 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 removed outlier: 3.605A pdb=" N ILE C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 76 " --> pdb=" O TYR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 105 through 126 removed outlier: 3.626A pdb=" N CYS C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 113 " --> pdb=" O PHE C 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 removed outlier: 4.204A pdb=" N GLU C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 3.857A pdb=" N ALA C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 220 removed outlier: 4.256A pdb=" N LYS C 220 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 253 removed outlier: 3.568A pdb=" N GLU C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Proline residue: C 243 - end of helix removed outlier: 4.580A pdb=" N GLU C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 removed outlier: 3.910A pdb=" N SER C 265 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 290 removed outlier: 3.535A pdb=" N HIS C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 285 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 319 removed outlier: 3.983A pdb=" N ALA C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 355 through 371 removed outlier: 4.780A pdb=" N ILE C 362 " --> pdb=" O TYR C 358 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 367 " --> pdb=" O LYS C 363 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.602A pdb=" N GLY E 20 " --> pdb=" O GLY E 17 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN E 21 " --> pdb=" O ASP E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 45 removed outlier: 3.706A pdb=" N MET E 37 " --> pdb=" O HIS E 33 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 43 " --> pdb=" O HIS E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 removed outlier: 3.811A pdb=" N MET E 51 " --> pdb=" O TYR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 66 removed outlier: 3.738A pdb=" N MET E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 79 removed outlier: 3.605A pdb=" N ILE E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 76 " --> pdb=" O TYR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 94 Processing helix chain 'E' and resid 105 through 126 removed outlier: 3.626A pdb=" N CYS E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 113 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 167 removed outlier: 4.204A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 165 " --> pdb=" O LEU E 161 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 removed outlier: 3.857A pdb=" N ALA E 186 " --> pdb=" O GLY E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 220 removed outlier: 4.256A pdb=" N LYS E 220 " --> pdb=" O GLY E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 253 removed outlier: 3.569A pdb=" N GLU E 238 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 4.580A pdb=" N GLU E 250 " --> pdb=" O SER E 246 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 266 removed outlier: 3.911A pdb=" N SER E 265 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 290 removed outlier: 3.535A pdb=" N HIS E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE E 287 " --> pdb=" O LYS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 319 removed outlier: 3.983A pdb=" N ALA E 309 " --> pdb=" O ILE E 305 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR E 314 " --> pdb=" O ARG E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 355 through 371 removed outlier: 4.781A pdb=" N ILE E 362 " --> pdb=" O TYR E 358 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE E 367 " --> pdb=" O LYS E 363 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU E 368 " --> pdb=" O GLN E 364 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN E 369 " --> pdb=" O ARG E 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 104 removed outlier: 3.565A pdb=" N LEU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Proline residue: A 76 - end of helix removed outlier: 3.858A pdb=" N GLU A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 126 removed outlier: 3.816A pdb=" N LEU A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 122 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 125 " --> pdb=" O ACYS A 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 130 removed outlier: 3.583A pdb=" N SER A 130 " --> pdb=" O LEU A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'B' and resid 63 through 105 removed outlier: 3.548A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.622A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.700A pdb=" N LEU B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 122 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 125 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 130 removed outlier: 3.586A pdb=" N SER B 130 " --> pdb=" O LEU B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 130' Processing helix chain 'F' and resid 724 through 728 removed outlier: 3.563A pdb=" N ARG F 728 " --> pdb=" O VAL F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 765 through 777 removed outlier: 3.604A pdb=" N VAL F 769 " --> pdb=" O LYS F 765 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU F 770 " --> pdb=" O GLN F 766 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS F 777 " --> pdb=" O LEU F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 799 removed outlier: 3.787A pdb=" N LEU F 792 " --> pdb=" O GLN F 788 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS F 793 " --> pdb=" O GLU F 789 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS F 794 " --> pdb=" O LEU F 790 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS F 796 " --> pdb=" O LEU F 792 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU F 797 " --> pdb=" O HIS F 793 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER F 798 " --> pdb=" O CYS F 794 " (cutoff:3.500A) Processing helix chain 'F' and resid 802 through 810 removed outlier: 4.025A pdb=" N LEU F 806 " --> pdb=" O ILE F 802 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS F 808 " --> pdb=" O GLU F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 827 removed outlier: 3.795A pdb=" N HIS F 826 " --> pdb=" O LEU F 822 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR F 827 " --> pdb=" O ALA F 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 822 through 827' Processing helix chain 'F' and resid 834 through 849 removed outlier: 3.926A pdb=" N ASN F 842 " --> pdb=" O ARG F 838 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA F 846 " --> pdb=" O ASN F 842 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE F 847 " --> pdb=" O LYS F 843 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR F 848 " --> pdb=" O GLY F 844 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 859 Processing helix chain 'F' and resid 863 through 874 removed outlier: 3.713A pdb=" N PHE F 870 " --> pdb=" O GLN F 866 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N TYR F 871 " --> pdb=" O CYS F 867 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR F 872 " --> pdb=" O VAL F 868 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR F 873 " --> pdb=" O GLU F 869 " (cutoff:3.500A) Processing helix chain 'F' and resid 875 through 879 removed outlier: 3.919A pdb=" N VAL F 878 " --> pdb=" O LYS F 875 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 728 removed outlier: 3.563A pdb=" N ARG D 728 " --> pdb=" O VAL D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 777 removed outlier: 3.605A pdb=" N VAL D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 770 " --> pdb=" O GLN D 766 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS D 777 " --> pdb=" O LEU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.786A pdb=" N LEU D 792 " --> pdb=" O GLN D 788 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS D 793 " --> pdb=" O GLU D 789 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS D 794 " --> pdb=" O LEU D 790 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS D 796 " --> pdb=" O LEU D 792 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU D 797 " --> pdb=" O HIS D 793 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER D 798 " --> pdb=" O CYS D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 802 through 810 removed outlier: 4.026A pdb=" N LEU D 806 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 808 " --> pdb=" O GLU D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 827 removed outlier: 3.795A pdb=" N HIS D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 822 through 827' Processing helix chain 'D' and resid 834 through 849 removed outlier: 3.926A pdb=" N ASN D 842 " --> pdb=" O ARG D 838 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 846 " --> pdb=" O ASN D 842 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE D 847 " --> pdb=" O LYS D 843 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 848 " --> pdb=" O GLY D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 859 Processing helix chain 'D' and resid 863 through 874 removed outlier: 3.713A pdb=" N PHE D 870 " --> pdb=" O GLN D 866 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR D 871 " --> pdb=" O CYS D 867 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR D 872 " --> pdb=" O VAL D 868 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 873 " --> pdb=" O GLU D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 879 removed outlier: 3.919A pdb=" N VAL D 878 " --> pdb=" O LYS D 875 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 193 through 195 removed outlier: 3.644A pdb=" N MET C 194 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU C 298 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU C 259 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 132 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS C 12 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE C 53 " --> pdb=" O VAL D 752 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 193 through 195 removed outlier: 3.644A pdb=" N MET E 194 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU E 298 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 259 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA E 132 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS E 12 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE E 53 " --> pdb=" O VAL F 752 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.29 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9246 1.03 - 1.23: 29 1.23 - 1.42: 4200 1.42 - 1.62: 5523 1.62 - 1.81: 100 Bond restraints: 19098 Sorted by residual: bond pdb=" CA ILE F 733 " pdb=" CB ILE F 733 " ideal model delta sigma weight residual 1.537 1.583 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" CA ILE D 733 " pdb=" CB ILE D 733 " ideal model delta sigma weight residual 1.537 1.583 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" O12 IHP C 501 " pdb=" P2 IHP C 501 " ideal model delta sigma weight residual 1.675 1.610 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O12 IHP E 501 " pdb=" P2 IHP E 501 " ideal model delta sigma weight residual 1.675 1.611 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O15 IHP C 501 " pdb=" P5 IHP C 501 " ideal model delta sigma weight residual 1.675 1.618 0.057 2.00e-02 2.50e+03 8.25e+00 ... (remaining 19093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 33550 1.68 - 3.36: 678 3.36 - 5.05: 132 5.05 - 6.73: 29 6.73 - 8.41: 15 Bond angle restraints: 34404 Sorted by residual: angle pdb=" C ASN E 369 " pdb=" N LEU E 370 " pdb=" CA LEU E 370 " ideal model delta sigma weight residual 120.28 127.58 -7.30 1.44e+00 4.82e-01 2.57e+01 angle pdb=" C ASN C 369 " pdb=" N LEU C 370 " pdb=" CA LEU C 370 " ideal model delta sigma weight residual 120.28 127.57 -7.29 1.44e+00 4.82e-01 2.56e+01 angle pdb=" C TYR C 358 " pdb=" N LEU C 359 " pdb=" CA LEU C 359 " ideal model delta sigma weight residual 120.44 126.55 -6.11 1.36e+00 5.41e-01 2.02e+01 angle pdb=" C TYR E 358 " pdb=" N LEU E 359 " pdb=" CA LEU E 359 " ideal model delta sigma weight residual 120.44 126.49 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ILE E 362 " pdb=" N LYS E 363 " pdb=" CA LYS E 363 " ideal model delta sigma weight residual 120.44 125.57 -5.13 1.30e+00 5.92e-01 1.56e+01 ... (remaining 34399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 8482 24.12 - 48.25: 469 48.25 - 72.37: 115 72.37 - 96.49: 15 96.49 - 120.61: 12 Dihedral angle restraints: 9093 sinusoidal: 4873 harmonic: 4220 Sorted by residual: dihedral pdb=" CA ASP F 745 " pdb=" C ASP F 745 " pdb=" N PRO F 746 " pdb=" CA PRO F 746 " ideal model delta harmonic sigma weight residual 180.00 145.50 34.50 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA ASP D 745 " pdb=" C ASP D 745 " pdb=" N PRO D 746 " pdb=" CA PRO D 746 " ideal model delta harmonic sigma weight residual 180.00 145.54 34.46 0 5.00e+00 4.00e-02 4.75e+01 dihedral pdb=" CA ASN C 326 " pdb=" C ASN C 326 " pdb=" N GLU C 327 " pdb=" CA GLU C 327 " ideal model delta harmonic sigma weight residual -180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 ... (remaining 9090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 1410 1.007 - 2.013: 0 2.013 - 3.020: 0 3.020 - 4.026: 0 4.026 - 5.033: 4 Chirality restraints: 1414 Sorted by residual: chirality pdb=" C2 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C2 IHP E 501 " pdb=" C1 IHP E 501 " pdb=" C3 IHP E 501 " pdb=" O12 IHP E 501 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C3 IHP E 501 " pdb=" C2 IHP E 501 " pdb=" C4 IHP E 501 " pdb=" O13 IHP E 501 " both_signs ideal model delta sigma weight residual False -2.34 2.39 -4.72 2.00e-01 2.50e+01 5.58e+02 ... (remaining 1411 not shown) Planarity restraints: 2840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 754 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO F 755 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 755 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 755 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 754 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 755 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 755 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 755 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 745 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 746 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 746 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 746 " 0.022 5.00e-02 4.00e+02 ... (remaining 2837 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 3582 2.30 - 3.01: 49413 3.01 - 3.72: 63114 3.72 - 4.43: 94411 4.43 - 5.14: 148506 Nonbonded interactions: 359026 Sorted by model distance: nonbonded pdb=" O LYS B 88 " pdb=" HZ1 LYS B 91 " model vdw 1.589 2.450 nonbonded pdb=" O PHE C 287 " pdb=" HG SER C 290 " model vdw 1.599 2.450 nonbonded pdb=" O PHE E 287 " pdb=" HG SER E 290 " model vdw 1.600 2.450 nonbonded pdb=" O TRP C 312 " pdb=" HG1 THR C 316 " model vdw 1.603 2.450 nonbonded pdb=" OE2 GLU D 837 " pdb=" HG1 THR D 861 " model vdw 1.613 2.450 ... (remaining 359021 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 'A' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) selection = (chain 'B' and (resid 62 through 70 or resid 72 through 76 or resid 78 through 1 \ 20 or resid 123 through 130)) } ncs_group { reference = (chain 'C' and (resid 8 through 325 or (resid 327 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 328 through 376 or r \ esid 501 through 504)) selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.330 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.700 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 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 : 0.005 0.065 9825 Z= 0.338 Angle : 0.832 8.412 13301 Z= 0.446 Chirality : 0.266 5.033 1414 Planarity : 0.004 0.051 1708 Dihedral : 16.347 120.615 3693 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.39 % Allowed : 2.76 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.23), residues: 1172 helix: -2.40 (0.19), residues: 405 sheet: -3.25 (0.43), residues: 100 loop : -1.92 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 753 HIS 0.005 0.001 HIS C 33 PHE 0.009 0.002 PHE C 205 TYR 0.017 0.002 TYR C 24 ARG 0.006 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 302 time to evaluate : 1.459 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: 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: 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: C 87 TYR cc_start: 0.4943 (m-80) cc_final: 0.4590 (m-80) REVERT: C 160 ILE cc_start: 0.7763 (mt) cc_final: 0.7505 (mt) REVERT: C 174 ASP cc_start: 0.7053 (t0) cc_final: 0.6842 (t0) REVERT: E 260 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7955 (tm-30) REVERT: E 297 MET cc_start: 0.6940 (mtp) cc_final: 0.6685 (ttm) REVERT: A 65 ILE cc_start: 0.6307 (pt) cc_final: 0.5982 (pt) REVERT: B 88 LYS cc_start: 0.8931 (mttt) cc_final: 0.8274 (tptt) REVERT: F 745 ASP cc_start: 0.4122 (t0) cc_final: 0.3347 (t0) REVERT: F 808 LYS cc_start: 0.6166 (mttt) cc_final: 0.5308 (ptpt) outliers start: 4 outliers final: 0 residues processed: 305 average time/residue: 0.5247 time to fit residues: 213.8154 Evaluate side-chains 211 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 HIS C 140 HIS C 292 ASN E 57 HIS E 92 GLN E 140 HIS ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN F 724 ASN D 724 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9825 Z= 0.208 Angle : 0.659 9.781 13301 Z= 0.333 Chirality : 0.041 0.472 1414 Planarity : 0.005 0.048 1708 Dihedral : 6.540 54.687 1391 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.79 % Allowed : 10.45 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.24), residues: 1172 helix: -0.86 (0.22), residues: 460 sheet: -3.11 (0.42), residues: 100 loop : -2.09 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 753 HIS 0.006 0.001 HIS E 375 PHE 0.008 0.001 PHE E 75 TYR 0.014 0.001 TYR C 24 ARG 0.008 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 231 time to evaluate : 1.511 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 TYR cc_start: 0.4855 (m-80) cc_final: 0.4475 (m-80) REVERT: C 174 ASP cc_start: 0.7401 (t0) cc_final: 0.6999 (t0) REVERT: C 249 MET cc_start: 0.6906 (mmp) cc_final: 0.6570 (mpp) REVERT: C 289 LYS cc_start: 0.8212 (tttm) cc_final: 0.7655 (tptp) REVERT: C 372 MET cc_start: 0.3639 (ttm) cc_final: 0.3295 (ppp) REVERT: E 140 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6647 (p90) REVERT: E 289 LYS cc_start: 0.7944 (tttm) cc_final: 0.7707 (tptm) REVERT: B 88 LYS cc_start: 0.9098 (mttt) cc_final: 0.8717 (tptt) REVERT: B 113 LEU cc_start: 0.8927 (mp) cc_final: 0.8692 (mp) REVERT: F 808 LYS cc_start: 0.5890 (mttt) cc_final: 0.5364 (ptpt) REVERT: F 849 LYS cc_start: 0.6529 (tptt) cc_final: 0.5534 (ttmt) outliers start: 8 outliers final: 4 residues processed: 234 average time/residue: 0.4463 time to fit residues: 146.4942 Evaluate side-chains 207 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 261 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 92 optimal weight: 0.0050 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 HIS C 167 HIS E 140 HIS E 167 HIS ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 826 HIS D 747 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9825 Z= 0.231 Angle : 0.624 8.941 13301 Z= 0.320 Chirality : 0.039 0.211 1414 Planarity : 0.004 0.045 1708 Dihedral : 6.460 59.413 1391 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.18 % Allowed : 13.02 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.24), residues: 1172 helix: -0.46 (0.22), residues: 472 sheet: -3.00 (0.46), residues: 100 loop : -2.18 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 753 HIS 0.015 0.002 HIS E 140 PHE 0.008 0.001 PHE B 92 TYR 0.014 0.001 TYR C 24 ARG 0.004 0.000 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 219 time to evaluate : 1.497 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 174 ASP cc_start: 0.7331 (t0) cc_final: 0.7006 (t0) REVERT: C 179 HIS cc_start: 0.8632 (t-90) cc_final: 0.8247 (t70) REVERT: C 204 TYR cc_start: 0.5954 (t80) cc_final: 0.5502 (t80) REVERT: C 251 MET cc_start: 0.5941 (mtp) cc_final: 0.5680 (mtp) REVERT: C 260 GLN cc_start: 0.8279 (tt0) cc_final: 0.7917 (tt0) REVERT: E 179 HIS cc_start: 0.8826 (t-90) cc_final: 0.8320 (t70) REVERT: A 80 GLU cc_start: 0.7264 (tp30) cc_final: 0.7004 (tp30) REVERT: A 111 GLU cc_start: 0.7872 (pp20) cc_final: 0.7533 (pp20) REVERT: B 88 LYS cc_start: 0.9057 (mttt) cc_final: 0.8814 (tptt) REVERT: F 808 LYS cc_start: 0.5946 (mttt) cc_final: 0.5629 (ptpt) REVERT: F 849 LYS cc_start: 0.6417 (tptt) cc_final: 0.5471 (ttmt) REVERT: D 870 PHE cc_start: 0.6388 (t80) cc_final: 0.6082 (t80) outliers start: 12 outliers final: 5 residues processed: 224 average time/residue: 0.4458 time to fit residues: 142.3310 Evaluate side-chains 200 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.0060 chunk 104 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9825 Z= 0.197 Angle : 0.596 8.111 13301 Z= 0.304 Chirality : 0.038 0.167 1414 Planarity : 0.004 0.046 1708 Dihedral : 6.442 58.347 1391 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 1.38 % Allowed : 15.38 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 1172 helix: -0.14 (0.22), residues: 492 sheet: -2.79 (0.50), residues: 100 loop : -2.17 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 753 HIS 0.005 0.001 HIS C 375 PHE 0.008 0.001 PHE B 92 TYR 0.011 0.001 TYR C 24 ARG 0.005 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 1.359 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 ARG cc_start: 0.8605 (mtp180) cc_final: 0.8180 (mtm110) REVERT: C 174 ASP cc_start: 0.7396 (t0) cc_final: 0.7104 (t0) REVERT: C 179 HIS cc_start: 0.8721 (t-90) cc_final: 0.8312 (t70) REVERT: E 179 HIS cc_start: 0.8849 (t-90) cc_final: 0.8371 (t70) REVERT: E 372 MET cc_start: 0.3134 (mtp) cc_final: 0.2756 (ptm) REVERT: A 111 GLU cc_start: 0.7994 (pp20) cc_final: 0.7758 (pp20) REVERT: B 84 THR cc_start: 0.8341 (p) cc_final: 0.8026 (p) REVERT: F 808 LYS cc_start: 0.6123 (mttt) cc_final: 0.5743 (ptpt) REVERT: F 849 LYS cc_start: 0.6412 (tptt) cc_final: 0.5526 (ttmt) REVERT: F 870 PHE cc_start: 0.6669 (t80) cc_final: 0.5801 (t80) REVERT: D 849 LYS cc_start: 0.6300 (tptt) cc_final: 0.5471 (ttmt) outliers start: 14 outliers final: 12 residues processed: 218 average time/residue: 0.4321 time to fit residues: 133.9930 Evaluate side-chains 209 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9825 Z= 0.254 Angle : 0.648 8.117 13301 Z= 0.337 Chirality : 0.039 0.159 1414 Planarity : 0.005 0.048 1708 Dihedral : 6.789 55.846 1391 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 1.78 % Allowed : 17.36 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.25), residues: 1172 helix: -0.02 (0.23), residues: 492 sheet: -2.84 (0.52), residues: 100 loop : -2.15 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 753 HIS 0.005 0.001 HIS C 179 PHE 0.014 0.002 PHE B 92 TYR 0.015 0.002 TYR C 204 ARG 0.005 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 1.347 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: 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: C 36 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8267 (ttp-110) REVERT: C 204 TYR cc_start: 0.6241 (t80) cc_final: 0.5952 (t80) REVERT: E 372 MET cc_start: 0.3277 (mtp) cc_final: 0.3019 (ptm) REVERT: B 84 THR cc_start: 0.8237 (p) cc_final: 0.7922 (p) REVERT: B 90 MET cc_start: 0.8111 (tpp) cc_final: 0.7574 (tpp) REVERT: F 808 LYS cc_start: 0.6125 (mttt) cc_final: 0.5851 (ptpt) REVERT: F 849 LYS cc_start: 0.6553 (tptt) cc_final: 0.5716 (ttmt) REVERT: F 870 PHE cc_start: 0.6898 (t80) cc_final: 0.6668 (t80) REVERT: D 849 LYS cc_start: 0.6220 (tptt) cc_final: 0.5616 (ttmt) outliers start: 18 outliers final: 14 residues processed: 219 average time/residue: 0.4339 time to fit residues: 134.8586 Evaluate side-chains 207 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9825 Z= 0.225 Angle : 0.626 7.842 13301 Z= 0.324 Chirality : 0.039 0.165 1414 Planarity : 0.004 0.044 1708 Dihedral : 6.686 56.247 1391 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 2.07 % Allowed : 18.15 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.25), residues: 1172 helix: -0.01 (0.23), residues: 488 sheet: -2.73 (0.53), residues: 100 loop : -2.23 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 753 HIS 0.004 0.001 HIS C 179 PHE 0.013 0.001 PHE F 852 TYR 0.014 0.001 TYR C 48 ARG 0.006 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 1.503 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: 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: C 36 ARG cc_start: 0.8449 (ttm110) cc_final: 0.8223 (ttp-110) REVERT: E 79 ILE cc_start: 0.7578 (tp) cc_final: 0.7325 (tt) REVERT: E 249 MET cc_start: 0.7173 (mmp) cc_final: 0.6831 (tmm) REVERT: E 372 MET cc_start: 0.3331 (mtp) cc_final: 0.2879 (ptm) REVERT: A 111 GLU cc_start: 0.7938 (pp20) cc_final: 0.7640 (pp20) REVERT: F 808 LYS cc_start: 0.6275 (mttt) cc_final: 0.6000 (ptpt) REVERT: F 849 LYS cc_start: 0.6618 (tptt) cc_final: 0.5775 (ttmt) REVERT: F 870 PHE cc_start: 0.6855 (t80) cc_final: 0.6623 (t80) REVERT: D 804 GLU cc_start: 0.7393 (tp30) cc_final: 0.7047 (tp30) REVERT: D 849 LYS cc_start: 0.6285 (tptt) cc_final: 0.5700 (ttmt) REVERT: D 870 PHE cc_start: 0.6260 (t80) cc_final: 0.5962 (t80) outliers start: 21 outliers final: 18 residues processed: 214 average time/residue: 0.4389 time to fit residues: 133.0143 Evaluate side-chains 213 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 68 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9825 Z= 0.215 Angle : 0.606 7.498 13301 Z= 0.314 Chirality : 0.038 0.165 1414 Planarity : 0.004 0.046 1708 Dihedral : 6.657 57.180 1391 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 1.97 % Allowed : 19.03 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.24), residues: 1172 helix: 0.01 (0.23), residues: 492 sheet: -2.68 (0.53), residues: 100 loop : -2.29 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 753 HIS 0.004 0.001 HIS E 179 PHE 0.014 0.001 PHE D 852 TYR 0.010 0.001 TYR C 48 ARG 0.006 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 1.609 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: 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: E 79 ILE cc_start: 0.7580 (tp) cc_final: 0.7320 (tt) REVERT: E 249 MET cc_start: 0.7183 (mmp) cc_final: 0.6820 (tmm) REVERT: A 111 GLU cc_start: 0.7915 (pp20) cc_final: 0.7662 (pp20) REVERT: F 808 LYS cc_start: 0.6173 (mttt) cc_final: 0.5951 (ptpt) REVERT: F 849 LYS cc_start: 0.6472 (tptt) cc_final: 0.5730 (ttmt) REVERT: D 804 GLU cc_start: 0.7514 (tp30) cc_final: 0.7211 (tp30) outliers start: 20 outliers final: 17 residues processed: 210 average time/residue: 0.4477 time to fit residues: 135.0309 Evaluate side-chains 212 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 811 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9825 Z= 0.215 Angle : 0.607 7.265 13301 Z= 0.316 Chirality : 0.038 0.166 1414 Planarity : 0.004 0.044 1708 Dihedral : 6.711 59.075 1391 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 2.07 % Allowed : 19.82 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.24), residues: 1172 helix: -0.00 (0.23), residues: 493 sheet: -2.66 (0.52), residues: 100 loop : -2.33 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 753 HIS 0.006 0.001 HIS C 179 PHE 0.037 0.002 PHE D 870 TYR 0.018 0.001 TYR D 827 ARG 0.006 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.452 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: 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: E 49 ARG cc_start: 0.8805 (mtp180) cc_final: 0.8377 (mtm110) REVERT: E 64 MET cc_start: 0.7507 (mmp) cc_final: 0.7290 (mmp) REVERT: E 79 ILE cc_start: 0.7660 (tp) cc_final: 0.7350 (tt) REVERT: E 249 MET cc_start: 0.7302 (mmp) cc_final: 0.6849 (tmm) REVERT: A 111 GLU cc_start: 0.7990 (pp20) cc_final: 0.7745 (pp20) REVERT: F 849 LYS cc_start: 0.6556 (tptt) cc_final: 0.6269 (tptt) REVERT: D 804 GLU cc_start: 0.7639 (tp30) cc_final: 0.7373 (tp30) REVERT: D 870 PHE cc_start: 0.6712 (t80) cc_final: 0.6507 (t80) outliers start: 21 outliers final: 17 residues processed: 210 average time/residue: 0.4267 time to fit residues: 127.3094 Evaluate side-chains 208 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 807 ASN Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9825 Z= 0.214 Angle : 0.616 6.928 13301 Z= 0.319 Chirality : 0.039 0.166 1414 Planarity : 0.005 0.046 1708 Dihedral : 6.737 59.835 1391 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 1.68 % Allowed : 20.71 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.24), residues: 1172 helix: 0.05 (0.23), residues: 491 sheet: -2.66 (0.52), residues: 100 loop : -2.32 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 753 HIS 0.005 0.001 HIS E 375 PHE 0.023 0.001 PHE D 870 TYR 0.028 0.001 TYR D 827 ARG 0.007 0.000 ARG F 838 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.391 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: 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: E 49 ARG cc_start: 0.8766 (mtp180) cc_final: 0.8297 (mtm110) REVERT: E 79 ILE cc_start: 0.7733 (tp) cc_final: 0.7426 (tt) REVERT: E 249 MET cc_start: 0.7252 (mmp) cc_final: 0.7046 (mmp) REVERT: A 111 GLU cc_start: 0.7914 (pp20) cc_final: 0.7638 (pp20) REVERT: B 90 MET cc_start: 0.8161 (tpp) cc_final: 0.7957 (tpp) REVERT: F 849 LYS cc_start: 0.6771 (tptt) cc_final: 0.6425 (tptt) REVERT: D 770 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6883 (pt0) REVERT: D 804 GLU cc_start: 0.7726 (tp30) cc_final: 0.7432 (tp30) outliers start: 17 outliers final: 15 residues processed: 204 average time/residue: 0.4487 time to fit residues: 129.4041 Evaluate side-chains 202 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 187 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN ** F 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9825 Z= 0.212 Angle : 0.617 7.704 13301 Z= 0.321 Chirality : 0.039 0.166 1414 Planarity : 0.005 0.044 1708 Dihedral : 6.706 59.953 1391 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 1.68 % Allowed : 20.41 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.24), residues: 1172 helix: 0.04 (0.23), residues: 492 sheet: -2.64 (0.51), residues: 100 loop : -2.32 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 753 HIS 0.005 0.001 HIS E 375 PHE 0.023 0.001 PHE D 870 TYR 0.018 0.001 TYR D 827 ARG 0.007 0.000 ARG F 838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Residue MET 736 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.504 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: 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: C 79 ILE cc_start: 0.7467 (tp) cc_final: 0.7158 (tt) REVERT: E 79 ILE cc_start: 0.7697 (tp) cc_final: 0.7373 (tt) REVERT: E 204 TYR cc_start: 0.6112 (t80) cc_final: 0.5674 (t80) REVERT: E 249 MET cc_start: 0.7341 (mmp) cc_final: 0.6827 (tmm) REVERT: A 111 GLU cc_start: 0.7988 (pp20) cc_final: 0.7760 (pp20) REVERT: B 90 MET cc_start: 0.8150 (tpp) cc_final: 0.7928 (tpp) REVERT: F 849 LYS cc_start: 0.6774 (tptt) cc_final: 0.6412 (tptt) REVERT: D 804 GLU cc_start: 0.7737 (tp30) cc_final: 0.7454 (tp30) outliers start: 17 outliers final: 15 residues processed: 203 average time/residue: 0.4857 time to fit residues: 139.2387 Evaluate side-chains 204 residues out of total 1027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain F residue 729 PHE Chi-restraints excluded: chain F residue 792 LEU Chi-restraints excluded: chain F residue 807 ASN Chi-restraints excluded: chain F residue 810 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 810 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.0370 chunk 37 optimal weight: 0.5980 chunk 93 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.165552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.144436 restraints weight = 76943.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.150227 restraints weight = 35426.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.154116 restraints weight = 20026.499| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4182 r_free = 0.4182 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9825 Z= 0.167 Angle : 0.586 6.709 13301 Z= 0.300 Chirality : 0.038 0.173 1414 Planarity : 0.004 0.045 1708 Dihedral : 6.454 58.435 1391 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.18 % Allowed : 21.10 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1172 helix: 0.09 (0.23), residues: 496 sheet: -2.35 (0.52), residues: 100 loop : -2.27 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 753 HIS 0.005 0.001 HIS E 375 PHE 0.019 0.001 PHE D 870 TYR 0.017 0.001 TYR D 827 ARG 0.007 0.000 ARG F 838 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4642.52 seconds wall clock time: 82 minutes 44.39 seconds (4964.39 seconds total)