Starting phenix.real_space_refine on Mon Dec 30 06:19:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t96_25752/12_2024/7t96_25752.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t96_25752/12_2024/7t96_25752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t96_25752/12_2024/7t96_25752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t96_25752/12_2024/7t96_25752.map" model { file = "/net/cci-nas-00/data/ceres_data/7t96_25752/12_2024/7t96_25752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t96_25752/12_2024/7t96_25752.cif" } resolution = 3.22 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4680 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 59 5.16 5 Cl 1 4.86 5 C 5382 2.51 5 N 1431 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8450 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2015 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 12, 'TRANS': 261} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2541 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "D" 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: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1747 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'2CU': 1, 'ACH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.81, per 1000 atoms: 0.69 Number of scatterers: 8450 At special positions: 0 Unit cell: (91.8, 121.55, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 59 16.00 O 1577 8.00 N 1431 7.00 C 5382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 176 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 36.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 22 through 50 removed outlier: 3.557A pdb=" N ILE A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.614A pdb=" N LEU A 54 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 55 " --> pdb=" O ARG A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 56 through 73 removed outlier: 3.703A pdb=" N TYR A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.827A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 94 removed outlier: 3.619A pdb=" N VAL A 94 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 91 through 94' Processing helix chain 'A' and resid 95 through 127 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.822A pdb=" N ARG A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 167 removed outlier: 3.653A pdb=" N ALA A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Proline residue: A 157 - end of helix removed outlier: 5.354A pdb=" N GLN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 212 Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 380 through 411 Proline residue: A 402 - end of helix removed outlier: 4.132A pdb=" N LEU A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 442 removed outlier: 4.209A pdb=" N ILE A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 426 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 433 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.516A pdb=" N THR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 31 removed outlier: 4.442A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.845A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 52' Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.711A pdb=" N LYS B 211 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 273 through 280 removed outlier: 4.246A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.076A pdb=" N ALA B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.765A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.834A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.800A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.519A pdb=" N PHE B 190 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 34 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 38 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ALA B 221 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.568A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.090A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.658A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.505A pdb=" N SER C 191 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.522A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.784A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.530A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.738A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 154 through 160 395 hydrogen bonds defined for protein. 1104 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: 2.63 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1364 1.28 - 1.41: 2209 1.41 - 1.55: 4967 1.55 - 1.69: 2 1.69 - 1.83: 85 Bond restraints: 8627 Sorted by residual: bond pdb=" C01 2CU A 502 " pdb=" N02 2CU A 502 " ideal model delta sigma weight residual 1.445 1.257 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C SER A 76 " pdb=" O SER A 76 " ideal model delta sigma weight residual 1.237 1.138 0.098 1.17e-02 7.31e+03 7.09e+01 bond pdb=" C TYR A 80 " pdb=" O TYR A 80 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.26e-02 6.30e+03 4.44e+01 bond pdb=" C24 2CU A 502 " pdb=" N26 2CU A 502 " ideal model delta sigma weight residual 1.353 1.481 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C08 2CU A 502 " pdb=" N05 2CU A 502 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.08e+01 ... (remaining 8622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 11399 2.40 - 4.81: 279 4.81 - 7.21: 50 7.21 - 9.61: 11 9.61 - 12.02: 7 Bond angle restraints: 11746 Sorted by residual: angle pdb=" N TYR A 80 " pdb=" CA TYR A 80 " pdb=" C TYR A 80 " ideal model delta sigma weight residual 111.82 99.80 12.02 1.16e+00 7.43e-01 1.07e+02 angle pdb=" N PRO A 418 " pdb=" CA PRO A 418 " pdb=" C PRO A 418 " ideal model delta sigma weight residual 113.53 101.66 11.87 1.39e+00 5.18e-01 7.29e+01 angle pdb=" N PHE A 61 " pdb=" CA PHE A 61 " pdb=" C PHE A 61 " ideal model delta sigma weight residual 112.54 102.43 10.11 1.22e+00 6.72e-01 6.87e+01 angle pdb=" N THR A 446 " pdb=" CA THR A 446 " pdb=" C THR A 446 " ideal model delta sigma weight residual 113.41 103.74 9.67 1.22e+00 6.72e-01 6.28e+01 angle pdb=" N THR A 420 " pdb=" CA THR A 420 " pdb=" C THR A 420 " ideal model delta sigma weight residual 114.62 106.97 7.65 1.14e+00 7.69e-01 4.51e+01 ... (remaining 11741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 4587 15.96 - 31.92: 358 31.92 - 47.88: 91 47.88 - 63.83: 14 63.83 - 79.79: 3 Dihedral angle restraints: 5053 sinusoidal: 1806 harmonic: 3247 Sorted by residual: dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 176 " pdb=" CB CYS A 176 " ideal model delta sinusoidal sigma weight residual -86.00 -162.75 76.75 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" C ASP B 273 " pdb=" N ASP B 273 " pdb=" CA ASP B 273 " pdb=" CB ASP B 273 " ideal model delta harmonic sigma weight residual -122.60 -110.83 -11.77 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA GLN C 75 " pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta harmonic sigma weight residual 180.00 156.86 23.14 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1195 0.080 - 0.159: 145 0.159 - 0.239: 19 0.239 - 0.319: 6 0.319 - 0.398: 4 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA ASP B 273 " pdb=" N ASP B 273 " pdb=" C ASP B 273 " pdb=" CB ASP B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CB VAL A 50 " pdb=" CA VAL A 50 " pdb=" CG1 VAL A 50 " pdb=" CG2 VAL A 50 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA THR A 420 " pdb=" N THR A 420 " pdb=" C THR A 420 " pdb=" CB THR A 420 " both_signs ideal model delta sigma weight residual False 2.53 2.86 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1366 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 409 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C ILE A 409 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE A 409 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 410 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 49 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" C LYS A 49 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 49 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL A 50 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 58 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C ASN A 58 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN A 58 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 59 " -0.017 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 163 2.65 - 3.21: 7904 3.21 - 3.78: 12292 3.78 - 4.34: 16635 4.34 - 4.90: 28016 Nonbonded interactions: 65010 Sorted by model distance: nonbonded pdb=" O ILE A 431 " pdb=" OG1 THR A 434 " model vdw 2.091 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.125 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.144 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.179 3.040 nonbonded pdb=" OE2 GLU C 215 " pdb=" NH2 ARG C 219 " model vdw 2.220 3.120 ... (remaining 65005 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.160 Find NCS groups from input model: 0.110 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.008 0.188 8627 Z= 0.529 Angle : 0.939 12.018 11746 Z= 0.573 Chirality : 0.059 0.398 1369 Planarity : 0.005 0.058 1479 Dihedral : 12.639 79.793 2950 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.35 % Allowed : 1.15 % Favored : 98.50 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1102 helix: 0.82 (0.28), residues: 349 sheet: -0.57 (0.32), residues: 269 loop : -1.82 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 99 HIS 0.006 0.002 HIS B 189 PHE 0.018 0.002 PHE E 68 TYR 0.019 0.002 TYR E 94 ARG 0.004 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8979 (mt) cc_final: 0.8738 (mp) REVERT: A 177 TYR cc_start: 0.7169 (p90) cc_final: 0.6856 (p90) REVERT: A 397 ILE cc_start: 0.8301 (mm) cc_final: 0.8087 (tt) REVERT: A 404 ASN cc_start: 0.8666 (m-40) cc_final: 0.8289 (m-40) REVERT: B 218 ASP cc_start: 0.7088 (t0) cc_final: 0.6847 (t0) REVERT: B 247 SER cc_start: 0.7795 (m) cc_final: 0.7535 (t) REVERT: B 250 LEU cc_start: 0.8012 (tp) cc_final: 0.7789 (tt) REVERT: B 272 LYS cc_start: 0.8563 (pttt) cc_final: 0.8238 (ttpt) REVERT: B 351 CYS cc_start: 0.7712 (m) cc_final: 0.7507 (m) REVERT: C 49 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7558 (mpt180) REVERT: C 198 LEU cc_start: 0.8466 (pt) cc_final: 0.8185 (pp) REVERT: C 239 ASN cc_start: 0.7623 (m-40) cc_final: 0.6461 (t0) REVERT: C 290 ASP cc_start: 0.6860 (m-30) cc_final: 0.6627 (m-30) outliers start: 3 outliers final: 3 residues processed: 250 average time/residue: 0.2145 time to fit residues: 72.0650 Evaluate side-chains 221 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 420 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 51 ASN B 194 ASN B 322 HIS C 75 GLN C 110 ASN E 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8627 Z= 0.230 Angle : 0.675 11.415 11746 Z= 0.345 Chirality : 0.045 0.223 1369 Planarity : 0.004 0.061 1479 Dihedral : 5.627 58.313 1217 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.84 % Allowed : 13.82 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.41 (0.26), residues: 1102 helix: 1.78 (0.29), residues: 340 sheet: -0.46 (0.32), residues: 281 loop : -1.69 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 212 HIS 0.004 0.001 HIS B 189 PHE 0.027 0.002 PHE A 181 TYR 0.017 0.001 TYR E 190 ARG 0.003 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.883 Fit side-chains REVERT: A 33 LEU cc_start: 0.8953 (mt) cc_final: 0.8575 (mp) REVERT: A 62 LEU cc_start: 0.8041 (tp) cc_final: 0.7782 (tp) REVERT: A 404 ASN cc_start: 0.8695 (m-40) cc_final: 0.8313 (m-40) REVERT: B 218 ASP cc_start: 0.6919 (t0) cc_final: 0.6694 (t0) REVERT: B 247 SER cc_start: 0.7773 (m) cc_final: 0.7554 (t) REVERT: B 272 LYS cc_start: 0.8624 (pttt) cc_final: 0.8259 (ttpt) REVERT: B 274 LEU cc_start: 0.8138 (tt) cc_final: 0.7886 (tt) REVERT: B 343 ILE cc_start: 0.8241 (mm) cc_final: 0.7988 (mt) REVERT: C 49 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7596 (mpt180) REVERT: C 198 LEU cc_start: 0.8370 (pt) cc_final: 0.8149 (pp) REVERT: C 239 ASN cc_start: 0.7634 (m-40) cc_final: 0.6505 (t0) REVERT: E 91 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8499 (p) REVERT: E 146 SER cc_start: 0.8220 (p) cc_final: 0.8012 (t) outliers start: 16 outliers final: 10 residues processed: 227 average time/residue: 0.2158 time to fit residues: 65.9568 Evaluate side-chains 223 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.0670 chunk 98 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8627 Z= 0.173 Angle : 0.617 11.090 11746 Z= 0.314 Chirality : 0.043 0.187 1369 Planarity : 0.004 0.060 1479 Dihedral : 5.012 53.429 1214 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.42 % Allowed : 17.28 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.16 (0.26), residues: 1102 helix: 2.07 (0.29), residues: 339 sheet: -0.38 (0.32), residues: 283 loop : -1.57 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 212 HIS 0.003 0.001 HIS B 196 PHE 0.021 0.001 PHE A 195 TYR 0.017 0.001 TYR E 190 ARG 0.006 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 1.347 Fit side-chains REVERT: A 62 LEU cc_start: 0.7969 (tp) cc_final: 0.7730 (tp) REVERT: A 404 ASN cc_start: 0.8648 (m-40) cc_final: 0.8317 (m-40) REVERT: B 218 ASP cc_start: 0.6857 (t0) cc_final: 0.6631 (t0) REVERT: B 272 LYS cc_start: 0.8566 (pttt) cc_final: 0.8211 (ttpt) REVERT: B 343 ILE cc_start: 0.8237 (mm) cc_final: 0.7981 (mt) REVERT: C 49 ARG cc_start: 0.7873 (mmt-90) cc_final: 0.7668 (mmt-90) REVERT: C 81 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6964 (mt) REVERT: C 219 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7576 (mmt-90) REVERT: C 239 ASN cc_start: 0.7516 (m110) cc_final: 0.6382 (t0) REVERT: E 101 TYR cc_start: 0.7747 (m-80) cc_final: 0.7422 (m-80) REVERT: E 140 MET cc_start: 0.8223 (mtm) cc_final: 0.7867 (mtt) outliers start: 21 outliers final: 10 residues processed: 230 average time/residue: 0.2223 time to fit residues: 68.9421 Evaluate side-chains 224 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 66 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8627 Z= 0.294 Angle : 0.667 11.157 11746 Z= 0.339 Chirality : 0.046 0.189 1369 Planarity : 0.004 0.067 1479 Dihedral : 5.164 57.769 1214 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.92 % Allowed : 17.63 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.12 (0.26), residues: 1102 helix: 2.12 (0.30), residues: 341 sheet: -0.44 (0.32), residues: 279 loop : -1.50 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 339 HIS 0.004 0.001 HIS B 189 PHE 0.023 0.002 PHE A 195 TYR 0.021 0.002 TYR E 190 ARG 0.007 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.849 Fit side-chains REVERT: A 62 LEU cc_start: 0.7956 (tp) cc_final: 0.7683 (tp) REVERT: A 389 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7670 (mt) REVERT: B 23 LEU cc_start: 0.8164 (mt) cc_final: 0.7961 (mp) REVERT: B 218 ASP cc_start: 0.6915 (t0) cc_final: 0.6697 (t0) REVERT: B 343 ILE cc_start: 0.8248 (mm) cc_final: 0.8008 (mt) REVERT: C 52 ARG cc_start: 0.7482 (ptp90) cc_final: 0.6883 (ptp90) REVERT: C 81 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7070 (mt) REVERT: C 239 ASN cc_start: 0.7624 (m-40) cc_final: 0.6451 (t0) REVERT: E 97 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7074 (t) REVERT: E 140 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7529 (mtm) outliers start: 34 outliers final: 20 residues processed: 230 average time/residue: 0.2144 time to fit residues: 66.4562 Evaluate side-chains 231 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8627 Z= 0.300 Angle : 0.670 11.093 11746 Z= 0.341 Chirality : 0.046 0.209 1369 Planarity : 0.004 0.069 1479 Dihedral : 5.222 58.922 1214 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.26 % Allowed : 19.01 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1102 helix: 2.04 (0.29), residues: 344 sheet: -0.43 (0.31), residues: 282 loop : -1.53 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 82 HIS 0.004 0.001 HIS B 189 PHE 0.024 0.002 PHE A 195 TYR 0.020 0.002 TYR E 190 ARG 0.003 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7949 (tp) cc_final: 0.7710 (tp) REVERT: A 72 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 389 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7718 (mt) REVERT: A 393 LEU cc_start: 0.7302 (tp) cc_final: 0.7069 (tt) REVERT: B 218 ASP cc_start: 0.6926 (t0) cc_final: 0.6698 (t0) REVERT: C 81 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7084 (mt) REVERT: C 239 ASN cc_start: 0.7672 (m-40) cc_final: 0.6479 (t0) REVERT: E 97 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7055 (t) REVERT: E 140 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7546 (mtm) REVERT: E 237 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8262 (mp) outliers start: 37 outliers final: 23 residues processed: 239 average time/residue: 0.2147 time to fit residues: 69.2292 Evaluate side-chains 241 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8627 Z= 0.226 Angle : 0.647 10.964 11746 Z= 0.327 Chirality : 0.044 0.190 1369 Planarity : 0.004 0.068 1479 Dihedral : 5.053 56.978 1214 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.26 % Allowed : 19.59 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.08 (0.26), residues: 1102 helix: 2.14 (0.30), residues: 342 sheet: -0.37 (0.31), residues: 280 loop : -1.52 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 212 HIS 0.004 0.001 HIS B 196 PHE 0.024 0.001 PHE A 195 TYR 0.018 0.001 TYR E 190 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.848 Fit side-chains REVERT: A 389 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7678 (mt) REVERT: A 393 LEU cc_start: 0.7253 (tp) cc_final: 0.7015 (tt) REVERT: A 450 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8105 (p) REVERT: B 218 ASP cc_start: 0.6895 (t0) cc_final: 0.6670 (t0) REVERT: B 343 ILE cc_start: 0.8252 (mm) cc_final: 0.8013 (mt) REVERT: C 81 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.7030 (mt) REVERT: E 97 VAL cc_start: 0.7415 (OUTLIER) cc_final: 0.6994 (t) REVERT: E 101 TYR cc_start: 0.7807 (m-80) cc_final: 0.7528 (m-80) REVERT: E 140 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7581 (mtm) REVERT: E 237 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8248 (mp) outliers start: 37 outliers final: 21 residues processed: 232 average time/residue: 0.2115 time to fit residues: 66.6092 Evaluate side-chains 229 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8627 Z= 0.212 Angle : 0.641 10.861 11746 Z= 0.323 Chirality : 0.044 0.222 1369 Planarity : 0.004 0.070 1479 Dihedral : 5.023 55.574 1214 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.69 % Allowed : 21.31 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.08 (0.26), residues: 1102 helix: 2.16 (0.30), residues: 343 sheet: -0.47 (0.31), residues: 285 loop : -1.48 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 212 HIS 0.004 0.001 HIS B 196 PHE 0.022 0.001 PHE A 195 TYR 0.017 0.001 TYR E 50 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.930 Fit side-chains REVERT: A 72 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 186 VAL cc_start: 0.8175 (t) cc_final: 0.7973 (p) REVERT: A 450 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 218 ASP cc_start: 0.6867 (t0) cc_final: 0.6660 (t0) REVERT: B 343 ILE cc_start: 0.8265 (mm) cc_final: 0.8014 (mt) REVERT: C 52 ARG cc_start: 0.7474 (ptp90) cc_final: 0.7158 (ptp90) REVERT: C 81 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7012 (mt) REVERT: E 97 VAL cc_start: 0.7421 (OUTLIER) cc_final: 0.6988 (t) REVERT: E 101 TYR cc_start: 0.7792 (m-80) cc_final: 0.7518 (m-80) REVERT: E 140 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7576 (mtm) REVERT: E 237 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8246 (mp) outliers start: 32 outliers final: 22 residues processed: 229 average time/residue: 0.2093 time to fit residues: 65.6358 Evaluate side-chains 228 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 237 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 chunk 91 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8627 Z= 0.205 Angle : 0.658 15.935 11746 Z= 0.326 Chirality : 0.044 0.249 1369 Planarity : 0.004 0.072 1479 Dihedral : 4.996 55.743 1214 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.26 % Allowed : 20.74 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.01 (0.26), residues: 1102 helix: 2.17 (0.29), residues: 345 sheet: -0.42 (0.31), residues: 284 loop : -1.42 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.021 0.001 PHE A 195 TYR 0.017 0.001 TYR E 190 ARG 0.011 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.957 Fit side-chains REVERT: A 72 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 389 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7647 (mt) REVERT: A 393 LEU cc_start: 0.7209 (tp) cc_final: 0.6972 (tt) REVERT: A 404 ASN cc_start: 0.8763 (m110) cc_final: 0.8359 (m-40) REVERT: A 450 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 343 ILE cc_start: 0.8301 (mm) cc_final: 0.8053 (mt) REVERT: C 81 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.7024 (mt) REVERT: C 246 ASP cc_start: 0.7066 (t70) cc_final: 0.6630 (t0) REVERT: E 97 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.6959 (t) REVERT: E 101 TYR cc_start: 0.7768 (m-80) cc_final: 0.7503 (m-80) REVERT: E 140 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7586 (mtm) outliers start: 37 outliers final: 24 residues processed: 221 average time/residue: 0.1968 time to fit residues: 60.6589 Evaluate side-chains 222 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 457 CYS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8627 Z= 0.262 Angle : 0.693 18.929 11746 Z= 0.344 Chirality : 0.045 0.243 1369 Planarity : 0.005 0.075 1479 Dihedral : 5.072 55.109 1213 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.26 % Allowed : 21.08 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.08 (0.26), residues: 1102 helix: 2.01 (0.29), residues: 349 sheet: -0.37 (0.31), residues: 281 loop : -1.46 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 148 HIS 0.004 0.001 HIS B 189 PHE 0.021 0.002 PHE A 195 TYR 0.019 0.001 TYR E 190 ARG 0.012 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.936 Fit side-chains REVERT: A 72 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8043 (tt) REVERT: A 389 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7705 (tp) REVERT: A 393 LEU cc_start: 0.7252 (tp) cc_final: 0.7033 (tt) REVERT: A 406 MET cc_start: 0.5269 (mtm) cc_final: 0.5042 (mtm) REVERT: B 343 ILE cc_start: 0.8258 (mm) cc_final: 0.8008 (mt) REVERT: C 52 ARG cc_start: 0.7470 (ptp90) cc_final: 0.7225 (ptp90) REVERT: C 81 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.7087 (mt) REVERT: C 219 ARG cc_start: 0.7768 (mmt-90) cc_final: 0.7495 (mmt-90) REVERT: C 262 MET cc_start: 0.7492 (ttm) cc_final: 0.7211 (mtp) REVERT: E 97 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7006 (t) REVERT: E 101 TYR cc_start: 0.7852 (m-80) cc_final: 0.7602 (m-80) REVERT: E 140 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7561 (mtm) outliers start: 37 outliers final: 26 residues processed: 225 average time/residue: 0.2073 time to fit residues: 64.6677 Evaluate side-chains 230 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8627 Z= 0.211 Angle : 0.671 17.984 11746 Z= 0.334 Chirality : 0.044 0.253 1369 Planarity : 0.004 0.075 1479 Dihedral : 4.996 53.609 1213 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.23 % Allowed : 22.12 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.01 (0.26), residues: 1102 helix: 2.07 (0.29), residues: 352 sheet: -0.35 (0.31), residues: 282 loop : -1.43 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.020 0.001 PHE A 195 TYR 0.017 0.001 TYR E 190 ARG 0.004 0.000 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.820 Fit side-chains REVERT: A 72 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 389 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 393 LEU cc_start: 0.7209 (tp) cc_final: 0.6977 (tt) REVERT: A 406 MET cc_start: 0.5207 (mtm) cc_final: 0.5000 (mtm) REVERT: B 343 ILE cc_start: 0.8292 (mm) cc_final: 0.8038 (mt) REVERT: C 52 ARG cc_start: 0.7463 (ptp90) cc_final: 0.7224 (ptp90) REVERT: C 81 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7046 (mt) REVERT: C 99 TRP cc_start: 0.8475 (m100) cc_final: 0.8153 (m100) REVERT: C 219 ARG cc_start: 0.7747 (mmt-90) cc_final: 0.7492 (mmt-90) REVERT: C 262 MET cc_start: 0.7507 (ttm) cc_final: 0.7294 (mtp) REVERT: C 263 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8017 (t) REVERT: E 97 VAL cc_start: 0.7386 (OUTLIER) cc_final: 0.6962 (t) REVERT: E 101 TYR cc_start: 0.7782 (m-80) cc_final: 0.7509 (m-80) REVERT: E 138 ILE cc_start: 0.8774 (mt) cc_final: 0.8541 (mp) REVERT: E 140 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7572 (mtm) outliers start: 28 outliers final: 22 residues processed: 222 average time/residue: 0.1998 time to fit residues: 61.1051 Evaluate side-chains 231 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 94 TYR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109930 restraints weight = 13556.454| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.25 r_work: 0.3342 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8627 Z= 0.234 Angle : 0.670 18.424 11746 Z= 0.336 Chirality : 0.045 0.242 1369 Planarity : 0.004 0.076 1479 Dihedral : 5.165 69.397 1213 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.69 % Allowed : 22.00 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1102 helix: 2.06 (0.29), residues: 352 sheet: -0.37 (0.31), residues: 289 loop : -1.51 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 148 HIS 0.004 0.001 HIS B 196 PHE 0.020 0.002 PHE A 195 TYR 0.018 0.001 TYR E 190 ARG 0.006 0.000 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2369.94 seconds wall clock time: 43 minutes 39.01 seconds (2619.01 seconds total)