Starting phenix.real_space_refine on Thu Mar 13 15:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0q_22608/03_2025/7k0q_22608.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0q_22608/03_2025/7k0q_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0q_22608/03_2025/7k0q_22608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0q_22608/03_2025/7k0q_22608.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0q_22608/03_2025/7k0q_22608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0q_22608/03_2025/7k0q_22608.cif" } resolution = 3.3 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= -0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.39, per 1000 atoms: 0.73 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: 2.56 Conformation dependent library (CDL) restraints added in 980.9 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: 0.87 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: 2.37 Time building geometry restraints manager: 2.90 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: 4951 17.94 - 35.89: 358 35.89 - 53.83: 61 53.83 - 71.77: 12 71.77 - 89.72: 3 Dihedral angle restraints: 5385 sinusoidal: 2182 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 5382 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: 4.100 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.006 0.048 8968 Z= 0.422 Angle : 0.700 8.754 12135 Z= 0.411 Chirality : 0.047 0.214 1352 Planarity : 0.004 0.061 1544 Dihedral : 12.739 89.718 3337 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), 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 TRP 0.012 0.002 TRP A 64 HIS 0.006 0.001 HIS A 292 PHE 0.019 0.002 PHE A 323 TYR 0.022 0.002 TYR A 166 ARG 0.006 0.001 ARG B 105 *********************** 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 : 0.922 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: 0.2206 time to fit residues: 36.7867 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 : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.0040 chunk 51 optimal weight: 0.0270 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092518 restraints weight = 13317.619| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.94 r_work: 0.2972 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8968 Z= 0.161 Angle : 0.499 6.696 12135 Z= 0.268 Chirality : 0.042 0.191 1352 Planarity : 0.004 0.052 1544 Dihedral : 4.824 49.489 1252 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.96 % Allowed : 6.42 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.25), residues: 1099 helix: 1.86 (0.23), residues: 536 sheet: -0.08 (0.45), residues: 122 loop : -0.69 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 86 HIS 0.004 0.001 HIS B 403 PHE 0.015 0.001 PHE A 323 TYR 0.014 0.001 TYR D 26 ARG 0.002 0.000 ARG B 95 *********************** 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 118 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.030 Fit side-chains REVERT: A 58 GLU cc_start: 0.8158 (mp0) cc_final: 0.7924 (mp0) REVERT: D 118 LYS cc_start: 0.7312 (mtpt) cc_final: 0.6721 (mttm) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.2481 time to fit residues: 39.3007 Evaluate side-chains 106 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.107812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091406 restraints weight = 13697.310| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.96 r_work: 0.2951 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8968 Z= 0.215 Angle : 0.487 7.292 12135 Z= 0.259 Chirality : 0.042 0.192 1352 Planarity : 0.004 0.049 1544 Dihedral : 4.498 47.353 1252 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.39 % Allowed : 7.28 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1099 helix: 1.91 (0.23), residues: 544 sheet: 0.02 (0.45), residues: 123 loop : -0.75 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 PHE 0.014 0.001 PHE A 209 TYR 0.012 0.001 TYR D 26 ARG 0.002 0.000 ARG A 287 *********************** 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 112 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.153 Fit side-chains REVERT: B 89 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: B 456 MET cc_start: 0.8570 (mtm) cc_final: 0.8277 (mtm) REVERT: D 118 LYS cc_start: 0.7376 (mtpt) cc_final: 0.6792 (mttm) REVERT: D 151 ASN cc_start: 0.9239 (t0) cc_final: 0.9009 (t0) outliers start: 13 outliers final: 8 residues processed: 104 average time/residue: 0.2399 time to fit residues: 35.6827 Evaluate side-chains 105 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 134 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.092026 restraints weight = 13460.990| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.95 r_work: 0.2960 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.192 Angle : 0.477 7.257 12135 Z= 0.254 Chirality : 0.042 0.185 1352 Planarity : 0.004 0.046 1544 Dihedral : 4.351 46.192 1252 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 8.57 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1099 helix: 2.03 (0.23), residues: 541 sheet: 0.04 (0.45), residues: 123 loop : -0.73 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 PHE 0.013 0.001 PHE A 209 TYR 0.012 0.001 TYR D 26 ARG 0.002 0.000 ARG B 136 *********************** 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: 16 poor density : 103 time to evaluate : 1.015 Fit side-chains REVERT: A 58 GLU cc_start: 0.8060 (mp0) cc_final: 0.7732 (mp0) REVERT: B 89 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8340 (m-30) REVERT: D 118 LYS cc_start: 0.7466 (mtpt) cc_final: 0.6896 (mttm) REVERT: D 151 ASN cc_start: 0.9194 (t0) cc_final: 0.8943 (t0) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 0.1937 time to fit residues: 31.0121 Evaluate side-chains 108 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 105 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090661 restraints weight = 13501.711| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.95 r_work: 0.2937 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8968 Z= 0.254 Angle : 0.499 7.572 12135 Z= 0.265 Chirality : 0.043 0.183 1352 Planarity : 0.004 0.046 1544 Dihedral : 4.366 44.897 1252 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.14 % Allowed : 8.99 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1099 helix: 1.99 (0.23), residues: 541 sheet: 0.04 (0.46), residues: 123 loop : -0.78 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.005 0.001 HIS A 292 PHE 0.014 0.001 PHE A 209 TYR 0.014 0.001 TYR B 235 ARG 0.002 0.000 ARG A 287 *********************** 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 120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.979 Fit side-chains REVERT: B 89 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: B 388 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8882 (mt) REVERT: D 118 LYS cc_start: 0.7460 (mtpt) cc_final: 0.6887 (mttm) REVERT: D 151 ASN cc_start: 0.9197 (t0) cc_final: 0.8938 (t0) outliers start: 20 outliers final: 11 residues processed: 108 average time/residue: 0.2073 time to fit residues: 32.6168 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 : 0.899 ------------------------------------------------------------------------------- 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 388 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 13 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 2 optimal weight: 0.0070 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092106 restraints weight = 13467.228| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.96 r_work: 0.2964 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.176 Angle : 0.470 8.378 12135 Z= 0.248 Chirality : 0.041 0.179 1352 Planarity : 0.004 0.043 1544 Dihedral : 4.238 45.263 1252 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.93 % Allowed : 9.96 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1099 helix: 2.16 (0.23), residues: 536 sheet: 0.06 (0.46), residues: 123 loop : -0.68 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 PHE 0.012 0.001 PHE A 209 TYR 0.017 0.001 TYR B 235 ARG 0.002 0.000 ARG A 151 *********************** 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 120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.005 Fit side-chains REVERT: A 58 GLU cc_start: 0.8096 (mp0) cc_final: 0.7807 (mp0) REVERT: B 89 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: B 388 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8819 (mt) REVERT: D 118 LYS cc_start: 0.7490 (mtpt) cc_final: 0.6937 (mttm) REVERT: D 151 ASN cc_start: 0.9193 (t0) cc_final: 0.8929 (t0) outliers start: 18 outliers final: 9 residues processed: 110 average time/residue: 0.1986 time to fit residues: 31.6833 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 : 1.001 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091308 restraints weight = 13517.082| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.99 r_work: 0.2953 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.207 Angle : 0.489 7.559 12135 Z= 0.256 Chirality : 0.042 0.179 1352 Planarity : 0.004 0.042 1544 Dihedral : 4.224 44.450 1252 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.71 % Allowed : 10.60 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1099 helix: 2.09 (0.23), residues: 542 sheet: 0.05 (0.47), residues: 123 loop : -0.71 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 PHE 0.013 0.001 PHE A 209 TYR 0.016 0.001 TYR B 235 ARG 0.002 0.000 ARG A 287 *********************** 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 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.243 Fit side-chains REVERT: A 58 GLU cc_start: 0.8108 (mp0) cc_final: 0.7775 (mp0) REVERT: B 89 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: B 388 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8820 (mt) REVERT: C 13 MET cc_start: 0.6267 (mmm) cc_final: 0.5820 (mmt) REVERT: D 118 LYS cc_start: 0.7507 (mtpt) cc_final: 0.6956 (mttm) REVERT: D 151 ASN cc_start: 0.9188 (t0) cc_final: 0.8931 (t0) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.1934 time to fit residues: 29.8678 Evaluate side-chains 111 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.091718 restraints weight = 13593.580| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.00 r_work: 0.2959 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.192 Angle : 0.483 8.888 12135 Z= 0.252 Chirality : 0.042 0.178 1352 Planarity : 0.004 0.041 1544 Dihedral : 4.188 44.446 1252 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 10.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1099 helix: 2.13 (0.23), residues: 542 sheet: 0.02 (0.47), residues: 123 loop : -0.70 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.003 0.001 HIS A 292 PHE 0.012 0.001 PHE A 209 TYR 0.014 0.001 TYR B 235 ARG 0.002 0.000 ARG A 151 *********************** 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 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.934 Fit side-chains REVERT: A 58 GLU cc_start: 0.8161 (mp0) cc_final: 0.7850 (mp0) REVERT: B 89 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: B 388 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8829 (mt) REVERT: C 13 MET cc_start: 0.6266 (mmm) cc_final: 0.6055 (mmt) REVERT: D 118 LYS cc_start: 0.7493 (mtpt) cc_final: 0.6946 (mttm) REVERT: D 151 ASN cc_start: 0.9179 (t0) cc_final: 0.8937 (t0) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.1929 time to fit residues: 30.2669 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 : 0.921 ------------------------------------------------------------------------------- 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 91 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.0470 chunk 91 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091653 restraints weight = 13577.168| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.97 r_work: 0.2957 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8968 Z= 0.208 Angle : 0.494 8.501 12135 Z= 0.258 Chirality : 0.042 0.178 1352 Planarity : 0.004 0.041 1544 Dihedral : 4.206 44.182 1252 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.82 % Allowed : 10.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1099 helix: 2.12 (0.23), residues: 542 sheet: -0.01 (0.46), residues: 123 loop : -0.72 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS A 292 PHE 0.013 0.001 PHE A 209 TYR 0.013 0.001 TYR B 235 ARG 0.002 0.000 ARG A 287 *********************** 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 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.918 Fit side-chains REVERT: A 58 GLU cc_start: 0.8148 (mp0) cc_final: 0.7816 (mp0) REVERT: B 89 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: B 388 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8834 (mt) REVERT: D 118 LYS cc_start: 0.7513 (mtpt) cc_final: 0.6966 (mttm) REVERT: D 151 ASN cc_start: 0.9178 (t0) cc_final: 0.8942 (t0) outliers start: 17 outliers final: 13 residues processed: 106 average time/residue: 0.1832 time to fit residues: 28.1532 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 : 0.898 ------------------------------------------------------------------------------- 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 91 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 76 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 72 optimal weight: 0.0020 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.093482 restraints weight = 13433.636| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.97 r_work: 0.2981 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8968 Z= 0.156 Angle : 0.468 8.502 12135 Z= 0.245 Chirality : 0.041 0.176 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.108 44.180 1252 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.82 % Allowed : 10.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1099 helix: 2.25 (0.23), residues: 536 sheet: 0.04 (0.46), residues: 123 loop : -0.66 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.002 0.000 HIS A 292 PHE 0.011 0.001 PHE A 209 TYR 0.013 0.001 TYR B 235 ARG 0.001 0.000 ARG A 151 ********************** 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 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.911 Fit side-chains REVERT: A 58 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: A 184 ILE cc_start: 0.8586 (mt) cc_final: 0.8372 (tp) REVERT: B 89 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: B 388 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8808 (mt) REVERT: D 118 LYS cc_start: 0.7510 (mtpt) cc_final: 0.6973 (mttm) REVERT: D 151 ASN cc_start: 0.9160 (t0) cc_final: 0.8946 (t0) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 0.1807 time to fit residues: 28.5662 Evaluate side-chains 112 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.122350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105915 restraints weight = 13517.274| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.86 r_work: 0.3170 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8968 Z= 0.171 Angle : 0.479 9.055 12135 Z= 0.248 Chirality : 0.041 0.176 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.093 43.655 1252 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.71 % Allowed : 10.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1099 helix: 2.23 (0.23), residues: 542 sheet: 0.06 (0.46), residues: 123 loop : -0.68 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 32 HIS 0.003 0.000 HIS A 292 PHE 0.012 0.001 PHE A 209 TYR 0.012 0.001 TYR B 235 ARG 0.001 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4253.87 seconds wall clock time: 75 minutes 39.38 seconds (4539.38 seconds total)