Starting phenix.real_space_refine on Fri Nov 15 02:57:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9s_35282/11_2024/8i9s_35282.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9s_35282/11_2024/8i9s_35282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9s_35282/11_2024/8i9s_35282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9s_35282/11_2024/8i9s_35282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9s_35282/11_2024/8i9s_35282.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9s_35282/11_2024/8i9s_35282.cif" } resolution = 3.26 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= 0.027 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5183 2.51 5 N 1402 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2046 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 261} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1558 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2427 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 403 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1689 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 5.60, per 1000 atoms: 0.69 Number of scatterers: 8123 At special positions: 0 Unit cell: (87.4526, 122.235, 124.223, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1484 8.00 N 1402 7.00 C 5183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 355 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'C' and resid 20 through 50 removed outlier: 3.826A pdb=" N SER C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 84 removed outlier: 3.865A pdb=" N ILE C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 removed outlier: 3.789A pdb=" N CYS C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Proline residue: C 99 - end of helix removed outlier: 5.089A pdb=" N VAL C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.887A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 154 removed outlier: 3.665A pdb=" N ALA C 139 " --> pdb=" O ASN C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 333 through 363 removed outlier: 5.889A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 373 through 403 removed outlier: 3.723A pdb=" N ARG C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.611A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 436 removed outlier: 6.348A pdb=" N LEU C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.083A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.551A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 215 " --> pdb=" O TRP A 212 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.689A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.536A pdb=" N SER H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.628A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.802A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 162 through 164 removed outlier: 3.856A pdb=" N GLU C 162 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 173 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 164 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 171 " --> pdb=" O PHE C 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.465A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.664A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.611A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.044A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.059A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.657A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.920A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.709A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.546A pdb=" N MET H 83 " --> pdb=" O ARG H 18 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.349A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 39 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.349A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 39 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.573A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.548A pdb=" N VAL H 226 " --> pdb=" O GLN H 179 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1173 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: 2.40 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2642 1.34 - 1.46: 2027 1.46 - 1.58: 3558 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8298 Sorted by residual: bond pdb=" C ILE C 98 " pdb=" N PRO C 99 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.28e+00 bond pdb=" C LEU C 38 " pdb=" N PRO C 39 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.30e-02 5.92e+03 1.06e+00 bond pdb=" C ILE C 155 " pdb=" N PRO C 156 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.72e-01 bond pdb=" C THR C 391 " pdb=" N PRO C 392 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.32e-01 bond pdb=" CB PRO A 315 " pdb=" CG PRO A 315 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.25e-01 ... (remaining 8293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 11049 1.50 - 2.99: 192 2.99 - 4.49: 48 4.49 - 5.99: 10 5.99 - 7.48: 8 Bond angle restraints: 11307 Sorted by residual: angle pdb=" CB MET C 27 " pdb=" CG MET C 27 " pdb=" SD MET C 27 " ideal model delta sigma weight residual 112.70 119.42 -6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" CA LEU A 274 " pdb=" CB LEU A 274 " pdb=" CG LEU A 274 " ideal model delta sigma weight residual 116.30 123.78 -7.48 3.50e+00 8.16e-02 4.57e+00 angle pdb=" C CYS A 325 " pdb=" N ALA A 326 " pdb=" CA ALA A 326 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.55e+00 angle pdb=" CB PRO G 60 " pdb=" CG PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 106.10 99.36 6.74 3.20e+00 9.77e-02 4.44e+00 angle pdb=" C ILE C 98 " pdb=" CA ILE C 98 " pdb=" CB ILE C 98 " ideal model delta sigma weight residual 114.00 111.27 2.73 1.31e+00 5.83e-01 4.33e+00 ... (remaining 11302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4419 16.92 - 33.85: 347 33.85 - 50.77: 68 50.77 - 67.69: 8 67.69 - 84.62: 6 Dihedral angle restraints: 4848 sinusoidal: 1641 harmonic: 3207 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 355 " pdb=" CB CYS C 355 " ideal model delta sinusoidal sigma weight residual 93.00 129.44 -36.44 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" CA PRO C 99 " pdb=" C PRO C 99 " pdb=" N SER C 100 " pdb=" CA SER C 100 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA TYR H 101 " pdb=" C TYR H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1099 0.056 - 0.112: 207 0.112 - 0.168: 15 0.168 - 0.224: 0 0.224 - 0.280: 1 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE A 266 " pdb=" N ILE A 266 " pdb=" C ILE A 266 " pdb=" CB ILE A 266 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1319 not shown) Planarity restraints: 1441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 314 " 0.057 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO A 315 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 20 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 21 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 21 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 21 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.030 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO G 60 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.025 5.00e-02 4.00e+02 ... (remaining 1438 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1794 2.79 - 3.32: 7330 3.32 - 3.84: 12601 3.84 - 4.37: 14066 4.37 - 4.90: 25704 Nonbonded interactions: 61495 Sorted by model distance: nonbonded pdb=" O ALA C 48 " pdb=" NH2 ARG C 54 " model vdw 2.260 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.264 3.040 nonbonded pdb=" OG1 THR C 55 " pdb=" OD1 ASN C 57 " model vdw 2.265 3.040 nonbonded pdb=" O CYS A 255 " pdb=" NZ LYS A 317 " model vdw 2.288 3.120 nonbonded pdb=" O LEU C 75 " pdb=" OG SER C 78 " model vdw 2.313 3.040 ... (remaining 61490 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.820 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 0.002 0.045 8298 Z= 0.153 Angle : 0.559 7.482 11307 Z= 0.290 Chirality : 0.042 0.280 1322 Planarity : 0.005 0.086 1441 Dihedral : 12.767 84.615 2766 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1095 helix: 1.96 (0.28), residues: 367 sheet: -0.25 (0.31), residues: 281 loop : -0.94 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 212 HIS 0.005 0.001 HIS C 394 PHE 0.018 0.001 PHE C 442 TYR 0.011 0.001 TYR H 101 ARG 0.008 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.841 Fit side-chains REVERT: C 27 MET cc_start: 0.5303 (mpp) cc_final: 0.3484 (tmm) REVERT: C 138 MET cc_start: 0.7544 (mmm) cc_final: 0.7189 (ttm) REVERT: C 414 MET cc_start: 0.4556 (ptt) cc_final: 0.4304 (ptt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1956 time to fit residues: 38.6559 Evaluate side-chains 105 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN H 39 GLN H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8298 Z= 0.273 Angle : 0.646 7.376 11307 Z= 0.339 Chirality : 0.046 0.183 1322 Planarity : 0.005 0.051 1441 Dihedral : 4.396 29.273 1182 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.52 % Allowed : 8.96 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1095 helix: 1.69 (0.28), residues: 377 sheet: -0.08 (0.31), residues: 274 loop : -1.25 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.006 0.001 HIS H 232 PHE 0.024 0.002 PHE B 234 TYR 0.014 0.002 TYR H 190 ARG 0.005 0.001 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.860 Fit side-chains REVERT: C 414 MET cc_start: 0.4598 (ptt) cc_final: 0.4396 (ptt) REVERT: A 53 MET cc_start: 0.6738 (mtm) cc_final: 0.6506 (mtm) REVERT: A 255 CYS cc_start: 0.7385 (p) cc_final: 0.7160 (p) REVERT: A 309 GLU cc_start: 0.5884 (tt0) cc_final: 0.5612 (tm-30) REVERT: B 154 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7641 (t0) REVERT: B 161 SER cc_start: 0.8840 (p) cc_final: 0.8633 (t) REVERT: H 80 PHE cc_start: 0.7829 (m-80) cc_final: 0.7434 (m-80) outliers start: 12 outliers final: 9 residues processed: 128 average time/residue: 0.1806 time to fit residues: 32.4758 Evaluate side-chains 117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8298 Z= 0.167 Angle : 0.535 6.366 11307 Z= 0.280 Chirality : 0.043 0.228 1322 Planarity : 0.004 0.046 1441 Dihedral : 3.978 28.073 1182 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.14 % Allowed : 11.74 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1095 helix: 1.83 (0.28), residues: 377 sheet: -0.22 (0.30), residues: 294 loop : -1.09 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE B 241 TYR 0.012 0.001 TYR H 190 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.938 Fit side-chains REVERT: C 414 MET cc_start: 0.4567 (ptt) cc_final: 0.4359 (ptt) REVERT: A 24 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8173 (tttp) REVERT: A 309 GLU cc_start: 0.5886 (tt0) cc_final: 0.5621 (tm-30) REVERT: B 154 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7609 (t0) REVERT: H 80 PHE cc_start: 0.7776 (m-80) cc_final: 0.7381 (m-80) outliers start: 9 outliers final: 6 residues processed: 130 average time/residue: 0.1635 time to fit residues: 31.3611 Evaluate side-chains 114 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8298 Z= 0.276 Angle : 0.618 6.966 11307 Z= 0.326 Chirality : 0.045 0.260 1322 Planarity : 0.004 0.048 1441 Dihedral : 4.396 31.502 1182 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.02 % Allowed : 13.26 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1095 helix: 1.66 (0.28), residues: 376 sheet: -0.14 (0.31), residues: 289 loop : -1.35 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS H 232 PHE 0.015 0.002 PHE B 241 TYR 0.015 0.002 TYR H 190 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.865 Fit side-chains REVERT: A 24 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8230 (tttp) REVERT: A 309 GLU cc_start: 0.5977 (tt0) cc_final: 0.5738 (tm-30) REVERT: B 45 MET cc_start: 0.8675 (mmm) cc_final: 0.8282 (mtt) REVERT: B 154 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7660 (t0) REVERT: B 214 ARG cc_start: 0.7582 (tpp-160) cc_final: 0.7296 (mmt-90) REVERT: H 80 PHE cc_start: 0.7958 (m-80) cc_final: 0.7681 (m-80) outliers start: 16 outliers final: 9 residues processed: 133 average time/residue: 0.1598 time to fit residues: 31.2116 Evaluate side-chains 123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.0370 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8298 Z= 0.182 Angle : 0.548 6.709 11307 Z= 0.286 Chirality : 0.043 0.227 1322 Planarity : 0.004 0.052 1441 Dihedral : 4.056 29.101 1182 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.89 % Allowed : 14.90 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1095 helix: 1.90 (0.28), residues: 370 sheet: -0.18 (0.30), residues: 295 loop : -1.14 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS H 232 PHE 0.013 0.001 PHE B 241 TYR 0.013 0.001 TYR H 190 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.852 Fit side-chains REVERT: A 24 LYS cc_start: 0.8485 (ttpp) cc_final: 0.8203 (tttp) REVERT: B 45 MET cc_start: 0.8687 (mmm) cc_final: 0.8287 (mtt) REVERT: B 154 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7689 (t0) REVERT: B 175 GLN cc_start: 0.7879 (mm110) cc_final: 0.7500 (mm-40) REVERT: B 214 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.7334 (mmt-90) REVERT: G 21 MET cc_start: 0.7651 (ttp) cc_final: 0.7400 (tmm) outliers start: 15 outliers final: 14 residues processed: 132 average time/residue: 0.1675 time to fit residues: 32.2648 Evaluate side-chains 126 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 0.0000 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 101 optimal weight: 0.0570 overall best weight: 0.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8298 Z= 0.134 Angle : 0.507 7.091 11307 Z= 0.262 Chirality : 0.042 0.279 1322 Planarity : 0.004 0.052 1441 Dihedral : 3.688 24.756 1182 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.15 % Allowed : 15.78 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1095 helix: 2.10 (0.29), residues: 371 sheet: 0.00 (0.31), residues: 287 loop : -1.05 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.000 HIS C 394 PHE 0.010 0.001 PHE B 241 TYR 0.011 0.001 TYR H 190 ARG 0.005 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.972 Fit side-chains REVERT: C 146 ILE cc_start: 0.7931 (mm) cc_final: 0.7715 (mt) REVERT: A 24 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8201 (tttp) REVERT: A 250 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8291 (tt) REVERT: B 45 MET cc_start: 0.8662 (mmm) cc_final: 0.8219 (mtt) REVERT: B 175 GLN cc_start: 0.7861 (mm110) cc_final: 0.7520 (mm-40) REVERT: G 21 MET cc_start: 0.7574 (ttp) cc_final: 0.7373 (tmm) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 0.1704 time to fit residues: 32.1153 Evaluate side-chains 118 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8298 Z= 0.227 Angle : 0.572 6.940 11307 Z= 0.298 Chirality : 0.045 0.285 1322 Planarity : 0.004 0.051 1441 Dihedral : 4.017 30.013 1182 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.15 % Allowed : 15.53 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1095 helix: 2.01 (0.28), residues: 371 sheet: 0.07 (0.31), residues: 286 loop : -1.13 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE B 241 TYR 0.013 0.001 TYR H 190 ARG 0.005 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.863 Fit side-chains REVERT: A 24 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8246 (tttp) REVERT: B 45 MET cc_start: 0.8653 (mmm) cc_final: 0.8300 (mtt) outliers start: 17 outliers final: 13 residues processed: 129 average time/residue: 0.1728 time to fit residues: 32.0333 Evaluate side-chains 127 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 PHE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 20 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8298 Z= 0.209 Angle : 0.571 10.092 11307 Z= 0.295 Chirality : 0.044 0.315 1322 Planarity : 0.004 0.052 1441 Dihedral : 4.036 30.499 1182 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.40 % Allowed : 15.28 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1095 helix: 1.96 (0.28), residues: 371 sheet: 0.09 (0.31), residues: 287 loop : -1.14 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS H 232 PHE 0.014 0.001 PHE B 241 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.873 Fit side-chains REVERT: A 24 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8241 (tttp) REVERT: A 250 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8326 (tt) REVERT: B 175 GLN cc_start: 0.8012 (mm110) cc_final: 0.7661 (mm-40) outliers start: 19 outliers final: 12 residues processed: 125 average time/residue: 0.1814 time to fit residues: 32.3243 Evaluate side-chains 117 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 PHE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8298 Z= 0.232 Angle : 0.585 6.948 11307 Z= 0.306 Chirality : 0.045 0.353 1322 Planarity : 0.004 0.053 1441 Dihedral : 4.158 31.286 1182 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.89 % Allowed : 16.29 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1095 helix: 1.90 (0.28), residues: 370 sheet: 0.16 (0.31), residues: 282 loop : -1.16 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS H 232 PHE 0.014 0.001 PHE B 241 TYR 0.013 0.001 TYR H 190 ARG 0.005 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.880 Fit side-chains REVERT: C 27 MET cc_start: 0.4950 (mtt) cc_final: 0.4580 (mmm) REVERT: A 24 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8217 (tttp) REVERT: A 250 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8321 (tt) REVERT: B 45 MET cc_start: 0.9141 (mtm) cc_final: 0.8768 (mtt) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.2010 time to fit residues: 34.4881 Evaluate side-chains 123 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 PHE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8298 Z= 0.179 Angle : 0.544 6.746 11307 Z= 0.284 Chirality : 0.044 0.332 1322 Planarity : 0.004 0.055 1441 Dihedral : 3.994 29.809 1182 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.52 % Allowed : 16.54 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1095 helix: 1.92 (0.28), residues: 371 sheet: 0.32 (0.31), residues: 276 loop : -1.13 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.002 0.001 HIS H 232 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR H 190 ARG 0.006 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.907 Fit side-chains REVERT: C 27 MET cc_start: 0.4937 (mtt) cc_final: 0.4610 (mmm) REVERT: A 24 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8174 (tttp) REVERT: A 250 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 45 MET cc_start: 0.9018 (mtm) cc_final: 0.8636 (mtt) REVERT: B 175 GLN cc_start: 0.8018 (mm110) cc_final: 0.7679 (mm110) outliers start: 12 outliers final: 11 residues processed: 119 average time/residue: 0.1892 time to fit residues: 32.5171 Evaluate side-chains 119 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 430 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134583 restraints weight = 10664.204| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.80 r_work: 0.3479 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8298 Z= 0.256 Angle : 0.600 7.162 11307 Z= 0.314 Chirality : 0.046 0.368 1322 Planarity : 0.004 0.056 1441 Dihedral : 4.227 31.547 1182 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.77 % Allowed : 16.92 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1095 helix: 1.78 (0.28), residues: 372 sheet: 0.17 (0.31), residues: 283 loop : -1.11 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS H 232 PHE 0.015 0.001 PHE B 241 TYR 0.013 0.002 TYR H 190 ARG 0.006 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.90 seconds wall clock time: 37 minutes 53.60 seconds (2273.60 seconds total)