Starting phenix.real_space_refine on Thu Jul 2 14:31:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.cif" model { file = "/net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0q_22608/07_2026/7k0q_22608.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.062 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 5647 2.51 5 N 1484 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8778 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3284 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1159 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 134} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLP': 1, 'VRP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.05, per 1000 atoms: 0.23 Number of scatterers: 8778 At special positions: 0 Unit cell: (89.445, 87.435, 119.595, 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) S 49 16.00 P 1 15.00 O 1597 8.00 N 1484 7.00 C 5647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 555.1 milliseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 55.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.568A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.673A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.516A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.537A pdb=" N SER A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.711A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.587A pdb=" N HIS A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.577A pdb=" N ILE A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.522A pdb=" N PHE A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 360 through 378 removed outlier: 4.342A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.702A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'B' and resid 67 through 94 removed outlier: 3.600A pdb=" N TRP B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.548A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.585A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix removed outlier: 3.556A pdb=" N VAL B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 457 removed outlier: 3.562A pdb=" N GLU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.111A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.524A pdb=" N LEU B 521 " --> pdb=" O THR B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 56 removed outlier: 4.063A pdb=" N PHE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.851A pdb=" N ILE D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 66 removed outlier: 3.555A pdb=" N THR D 66 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.507A pdb=" N LEU D 82 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 117 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 removed outlier: 3.860A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 146 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.938A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.714A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.214A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.736A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.668A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.998A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1266 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: 1.45 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2784 1.34 - 1.46: 1345 1.46 - 1.57: 4755 1.57 - 1.69: 3 1.69 - 1.81: 81 Bond restraints: 8968 Sorted by residual: bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.16e-02 7.43e+03 7.00e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.13e+00 bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 6.00e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.73e+00 bond pdb=" C18 VRP B 602 " pdb=" C19 VRP B 602 " ideal model delta sigma weight residual 1.538 1.578 -0.040 2.00e-02 2.50e+03 4.09e+00 ... (remaining 8963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 11776 1.75 - 3.50: 307 3.50 - 5.25: 44 5.25 - 7.00: 5 7.00 - 8.75: 3 Bond angle restraints: 12135 Sorted by residual: angle pdb=" CA GLY B 385 " pdb=" C GLY B 385 " pdb=" N GLY B 386 " ideal model delta sigma weight residual 114.23 117.30 -3.07 8.80e-01 1.29e+00 1.22e+01 angle pdb=" C TYR B 474 " pdb=" N MET B 475 " pdb=" CA MET B 475 " ideal model delta sigma weight residual 122.74 114.47 8.27 2.44e+00 1.68e-01 1.15e+01 angle pdb=" C ARG A 422 " pdb=" N SER A 423 " pdb=" CA SER A 423 " ideal model delta sigma weight residual 122.74 127.52 -4.78 1.44e+00 4.82e-01 1.10e+01 angle pdb=" N TYR B 474 " pdb=" CA TYR B 474 " pdb=" CB TYR B 474 " ideal model delta sigma weight residual 114.17 110.70 3.47 1.14e+00 7.69e-01 9.26e+00 angle pdb=" N ASN D 151 " pdb=" CA ASN D 151 " pdb=" C ASN D 151 " ideal model delta sigma weight residual 112.86 109.15 3.71 1.22e+00 6.72e-01 9.23e+00 ... (remaining 12130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4936 17.94 - 35.89: 355 35.89 - 53.83: 56 53.83 - 71.77: 12 71.77 - 89.72: 3 Dihedral angle restraints: 5362 sinusoidal: 2159 harmonic: 3203 Sorted by residual: dihedral pdb=" CA ARG B 105 " pdb=" C ARG B 105 " pdb=" N GLU B 106 " pdb=" CA GLU B 106 " ideal model delta harmonic sigma weight residual -180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA SER B 506 " pdb=" C SER B 506 " pdb=" N ARG B 507 " pdb=" CA ARG B 507 " ideal model delta harmonic sigma weight residual 180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA TYR B 115 " pdb=" C TYR B 115 " pdb=" N GLN B 116 " pdb=" CA GLN B 116 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 936 0.043 - 0.085: 309 0.085 - 0.128: 90 0.128 - 0.171: 15 0.171 - 0.214: 2 Chirality restraints: 1352 Sorted by residual: chirality pdb=" C18 VRP B 602 " pdb=" C17 VRP B 602 " pdb=" C19 VRP B 602 " pdb=" O28 VRP B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE B 503 " pdb=" CA ILE B 503 " pdb=" CG1 ILE B 503 " pdb=" CG2 ILE B 503 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 1349 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO B 413 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 470 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 58 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU A 58 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 58 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 58 " 0.010 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 119 2.67 - 3.23: 8341 3.23 - 3.79: 12833 3.79 - 4.34: 17426 4.34 - 4.90: 30250 Nonbonded interactions: 68969 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" O24 VRP B 602 " model vdw 2.116 3.040 nonbonded pdb=" NH2 ARG B 105 " pdb=" OE2 GLU B 107 " model vdw 2.227 3.120 nonbonded pdb=" NH2 ARG A 422 " pdb=" OE1 GLU A 466 " model vdw 2.255 3.120 nonbonded pdb=" O ARG A 422 " pdb=" OG SER A 423 " model vdw 2.256 3.040 nonbonded pdb=" OG1 THR D 74 " pdb=" OD1 ASP D 76 " model vdw 2.268 3.040 ... (remaining 68964 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: 5.330 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.100 Find NCS groups from input model: 0.050 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:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 8969 Z= 0.308 Angle : 0.700 8.754 12135 Z= 0.411 Chirality : 0.047 0.214 1352 Planarity : 0.004 0.061 1544 Dihedral : 12.642 89.718 3314 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.25), residues: 1099 helix: 1.43 (0.23), residues: 537 sheet: -0.30 (0.44), residues: 124 loop : -0.91 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 105 TYR 0.022 0.002 TYR A 166 PHE 0.019 0.002 PHE A 323 TRP 0.012 0.002 TRP A 64 HIS 0.006 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.28 ( 8968) covalent geometry : angle 0.69974 / 0.41 (12135) hydrogen bonds : bond 0.14747 / 10.04 ( 444) hydrogen bonds : angle 5.37754 / 3.74 ( 1266) Misc. bond : bond 0.11435 / 6.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.351 Fit side-chains REVERT: B 304 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.6771 (ptt90) REVERT: D 118 LYS cc_start: 0.7109 (mtpt) cc_final: 0.6591 (mttm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.0930 time to fit residues: 15.6376 Evaluate side-chains 99 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0040 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091878 restraints weight = 13520.395| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.96 r_work: 0.2962 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8969 Z= 0.126 Angle : 0.507 6.767 12135 Z= 0.272 Chirality : 0.042 0.198 1352 Planarity : 0.004 0.053 1544 Dihedral : 4.767 47.897 1229 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.96 % Allowed : 6.32 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1099 helix: 1.83 (0.23), residues: 536 sheet: -0.10 (0.45), residues: 122 loop : -0.73 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.015 0.001 TYR A 166 PHE 0.015 0.001 PHE A 323 TRP 0.007 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8968) covalent geometry : angle 0.50707 / 0.27 (12135) hydrogen bonds : bond 0.04423 / 3.15 ( 444) hydrogen bonds : angle 4.29333 / 3.02 ( 1266) Misc. bond : bond 0.00111 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.348 Fit side-chains REVERT: A 58 GLU cc_start: 0.8164 (mp0) cc_final: 0.7925 (mp0) REVERT: D 118 LYS cc_start: 0.7372 (mtpt) cc_final: 0.6782 (mttm) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.0945 time to fit residues: 14.9144 Evaluate side-chains 103 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091907 restraints weight = 13516.836| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.95 r_work: 0.2958 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8969 Z= 0.123 Angle : 0.478 7.050 12135 Z= 0.254 Chirality : 0.042 0.191 1352 Planarity : 0.004 0.048 1544 Dihedral : 4.427 46.794 1229 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.18 % Allowed : 7.71 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1099 helix: 1.92 (0.23), residues: 544 sheet: 0.04 (0.45), residues: 123 loop : -0.75 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.012 0.001 TYR D 26 PHE 0.013 0.001 PHE A 209 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8968) covalent geometry : angle 0.47764 / 0.25 (12135) hydrogen bonds : bond 0.04216 / 2.99 ( 444) hydrogen bonds : angle 4.13179 / 2.91 ( 1266) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.351 Fit side-chains REVERT: B 89 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: B 456 MET cc_start: 0.8587 (mtm) cc_final: 0.8313 (mtm) REVERT: D 118 LYS cc_start: 0.7382 (mtpt) cc_final: 0.6797 (mttm) REVERT: D 151 ASN cc_start: 0.9247 (t0) cc_final: 0.9020 (t0) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.0858 time to fit residues: 13.3057 Evaluate side-chains 104 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092147 restraints weight = 13660.705| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.96 r_work: 0.2958 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8969 Z= 0.128 Angle : 0.485 7.288 12135 Z= 0.256 Chirality : 0.042 0.184 1352 Planarity : 0.004 0.046 1544 Dihedral : 4.315 45.279 1229 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.82 % Allowed : 8.78 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1099 helix: 2.00 (0.23), residues: 543 sheet: 0.04 (0.46), residues: 123 loop : -0.76 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.012 0.001 TYR D 26 PHE 0.013 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8968) covalent geometry : angle 0.48456 / 0.26 (12135) hydrogen bonds : bond 0.04107 / 2.91 ( 444) hydrogen bonds : angle 4.05550 / 2.85 ( 1266) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.262 Fit side-chains REVERT: A 58 GLU cc_start: 0.8067 (mp0) cc_final: 0.7734 (mp0) REVERT: B 89 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8333 (m-30) REVERT: D 118 LYS cc_start: 0.7461 (mtpt) cc_final: 0.6889 (mttm) REVERT: D 151 ASN cc_start: 0.9220 (t0) cc_final: 0.8981 (t0) outliers start: 17 outliers final: 10 residues processed: 110 average time/residue: 0.0883 time to fit residues: 13.9074 Evaluate side-chains 110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.0270 chunk 18 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107296 restraints weight = 13519.941| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.89 r_work: 0.3177 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8969 Z= 0.100 Angle : 0.456 7.047 12135 Z= 0.241 Chirality : 0.041 0.179 1352 Planarity : 0.004 0.043 1544 Dihedral : 4.163 44.873 1229 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.61 % Allowed : 9.42 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1099 helix: 2.15 (0.23), residues: 541 sheet: 0.10 (0.46), residues: 123 loop : -0.70 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.014 0.001 TYR B 235 PHE 0.011 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.002 0.000 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 8968) covalent geometry : angle 0.45573 / 0.24 (12135) hydrogen bonds : bond 0.03567 / 2.55 ( 444) hydrogen bonds : angle 3.96116 / 2.78 ( 1266) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.262 Fit side-chains REVERT: B 89 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: B 388 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8837 (mt) REVERT: D 118 LYS cc_start: 0.7536 (mtpt) cc_final: 0.6988 (mttm) REVERT: D 151 ASN cc_start: 0.9203 (t0) cc_final: 0.8981 (t0) outliers start: 15 outliers final: 9 residues processed: 108 average time/residue: 0.0852 time to fit residues: 13.2775 Evaluate side-chains 110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106048 restraints weight = 13670.444| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.91 r_work: 0.3155 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8969 Z= 0.125 Angle : 0.484 8.285 12135 Z= 0.252 Chirality : 0.042 0.179 1352 Planarity : 0.004 0.041 1544 Dihedral : 4.143 44.315 1229 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.82 % Allowed : 10.28 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1099 helix: 2.16 (0.23), residues: 541 sheet: 0.10 (0.46), residues: 123 loop : -0.72 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.016 0.001 TYR B 235 PHE 0.012 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8968) covalent geometry : angle 0.48402 / 0.25 (12135) hydrogen bonds : bond 0.03922 / 2.77 ( 444) hydrogen bonds : angle 3.94926 / 2.77 ( 1266) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.354 Fit side-chains REVERT: A 58 GLU cc_start: 0.8090 (mp0) cc_final: 0.7847 (mp0) REVERT: B 89 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8373 (m-30) REVERT: B 388 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8818 (mt) REVERT: C 13 MET cc_start: 0.6217 (mmm) cc_final: 0.6016 (mmt) REVERT: D 118 LYS cc_start: 0.7554 (mtpt) cc_final: 0.7005 (mttm) REVERT: D 151 ASN cc_start: 0.9205 (t0) cc_final: 0.8974 (t0) outliers start: 17 outliers final: 10 residues processed: 108 average time/residue: 0.0807 time to fit residues: 12.8134 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 0.0050 chunk 59 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.3332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108239 restraints weight = 13545.792| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.91 r_work: 0.3189 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8969 Z= 0.094 Angle : 0.456 7.422 12135 Z= 0.238 Chirality : 0.041 0.176 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.033 44.298 1229 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.71 % Allowed : 10.39 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1099 helix: 2.31 (0.23), residues: 536 sheet: 0.01 (0.47), residues: 125 loop : -0.64 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.012 0.001 TYR B 235 PHE 0.010 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 8968) covalent geometry : angle 0.45610 / 0.24 (12135) hydrogen bonds : bond 0.03333 / 2.38 ( 444) hydrogen bonds : angle 3.87495 / 2.72 ( 1266) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.343 Fit side-chains REVERT: A 58 GLU cc_start: 0.8041 (mp0) cc_final: 0.7767 (mp0) REVERT: A 184 ILE cc_start: 0.8733 (mt) cc_final: 0.8504 (tt) REVERT: B 89 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: B 388 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8788 (mt) REVERT: B 529 ASP cc_start: 0.8633 (t0) cc_final: 0.8426 (t0) REVERT: D 118 LYS cc_start: 0.7559 (mtpt) cc_final: 0.7021 (mttm) REVERT: D 151 ASN cc_start: 0.9182 (t0) cc_final: 0.8978 (t0) outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.0897 time to fit residues: 14.5753 Evaluate side-chains 112 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 72 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105924 restraints weight = 13446.730| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.85 r_work: 0.3169 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8969 Z= 0.120 Angle : 0.479 8.866 12135 Z= 0.248 Chirality : 0.041 0.176 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.038 43.593 1229 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.61 % Allowed : 10.92 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1099 helix: 2.22 (0.23), residues: 542 sheet: 0.11 (0.47), residues: 123 loop : -0.68 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.016 0.001 TYR B 235 PHE 0.012 0.001 PHE A 209 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8968) covalent geometry : angle 0.47911 / 0.25 (12135) hydrogen bonds : bond 0.03750 / 2.65 ( 444) hydrogen bonds : angle 3.88038 / 2.72 ( 1266) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.343 Fit side-chains REVERT: A 58 GLU cc_start: 0.8125 (mp0) cc_final: 0.7874 (mp0) REVERT: B 89 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8365 (m-30) REVERT: B 388 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8803 (mt) REVERT: D 118 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7020 (mttm) REVERT: D 151 ASN cc_start: 0.9184 (t0) cc_final: 0.8965 (t0) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.0848 time to fit residues: 13.3888 Evaluate side-chains 110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.0010 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106500 restraints weight = 13397.557| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.89 r_work: 0.3164 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8969 Z= 0.120 Angle : 0.487 8.530 12135 Z= 0.251 Chirality : 0.041 0.176 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.046 43.842 1229 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.82 % Allowed : 10.81 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1099 helix: 2.24 (0.23), residues: 542 sheet: 0.09 (0.46), residues: 123 loop : -0.68 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.016 0.001 TYR B 235 PHE 0.012 0.001 PHE A 209 TRP 0.010 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8968) covalent geometry : angle 0.48723 / 0.25 (12135) hydrogen bonds : bond 0.03771 / 2.67 ( 444) hydrogen bonds : angle 3.88597 / 2.72 ( 1266) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.315 Fit side-chains REVERT: A 58 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: A 451 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: B 89 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: B 388 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8810 (mt) REVERT: C 13 MET cc_start: 0.6483 (mmm) cc_final: 0.6171 (mmt) REVERT: D 118 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7041 (mttm) REVERT: D 151 ASN cc_start: 0.9184 (t0) cc_final: 0.8971 (t0) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.0828 time to fit residues: 12.8512 Evaluate side-chains 110 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 0.0010 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107077 restraints weight = 13531.449| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.91 r_work: 0.3172 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8969 Z= 0.111 Angle : 0.483 8.433 12135 Z= 0.248 Chirality : 0.041 0.176 1352 Planarity : 0.004 0.039 1544 Dihedral : 4.017 43.825 1229 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.61 % Allowed : 10.92 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1099 helix: 2.26 (0.23), residues: 542 sheet: 0.10 (0.46), residues: 123 loop : -0.69 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 304 TYR 0.016 0.001 TYR B 235 PHE 0.012 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8968) covalent geometry : angle 0.48293 / 0.25 (12135) hydrogen bonds : bond 0.03625 / 2.58 ( 444) hydrogen bonds : angle 3.86383 / 2.71 ( 1266) Misc. bond : bond 0.00014 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.352 Fit side-chains REVERT: A 58 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: A 451 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: B 89 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8357 (m-30) REVERT: B 388 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8809 (mt) REVERT: C 13 MET cc_start: 0.6467 (mmm) cc_final: 0.6167 (mmt) REVERT: D 118 LYS cc_start: 0.7569 (mtpt) cc_final: 0.7041 (mttm) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.0850 time to fit residues: 13.4477 Evaluate side-chains 109 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 0.9990 chunk 21 optimal weight: 0.0010 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.124609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107879 restraints weight = 13422.632| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.89 r_work: 0.3188 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8969 Z= 0.102 Angle : 0.482 8.523 12135 Z= 0.248 Chirality : 0.041 0.190 1352 Planarity : 0.004 0.039 1544 Dihedral : 3.982 43.820 1229 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.61 % Allowed : 11.13 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1099 helix: 2.35 (0.23), residues: 536 sheet: -0.00 (0.46), residues: 125 loop : -0.63 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 304 TYR 0.016 0.001 TYR B 235 PHE 0.011 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 8968) covalent geometry : angle 0.48163 / 0.25 (12135) hydrogen bonds : bond 0.03453 / 2.46 ( 444) hydrogen bonds : angle 3.84421 / 2.69 ( 1266) Misc. bond : bond 0.00012 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.95 seconds wall clock time: 37 minutes 59.85 seconds (2279.85 seconds total)