Starting phenix.real_space_refine on Sun Apr 5 07:34:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0q_22608/04_2026/7k0q_22608.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0q_22608/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k0q_22608/04_2026/7k0q_22608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0q_22608/04_2026/7k0q_22608.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0q_22608/04_2026/7k0q_22608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0q_22608/04_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-2.1rc1-6017/lib/python3.9/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: 2.07, per 1000 atoms: 0.24 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: 0.64 Conformation dependent library (CDL) restraints added in 369.5 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: 0.37 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: 0.89 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: 6.090 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- 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 : 0.007 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 : 12.739 89.718 3337 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 covalent geometry : bond 0.00645 ( 8968) covalent geometry : angle 0.69974 (12135) hydrogen bonds : bond 0.14747 ( 444) hydrogen bonds : angle 5.37754 ( 1266) Misc. bond : bond 0.11435 ( 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 : 0.265 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: 0.0950 time to fit residues: 15.7333 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 : 0.350 ------------------------------------------------------------------------------- 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... 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 = 0.108210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.091773 restraints weight = 13532.011| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.95 r_work: 0.2957 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0933 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 : 0.508 6.807 12135 Z= 0.273 Chirality : 0.043 0.193 1352 Planarity : 0.004 0.053 1544 Dihedral : 4.865 48.610 1252 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: 0.89 (0.25), residues: 1099 helix: 1.82 (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 B 131 TYR 0.015 0.001 TYR A 166 PHE 0.015 0.001 PHE A 323 TRP 0.008 0.001 TRP C 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8968) covalent geometry : angle 0.50833 (12135) hydrogen bonds : bond 0.04585 ( 444) hydrogen bonds : angle 4.32329 ( 1266) Misc. bond : bond 0.00032 ( 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 118 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.327 Fit side-chains REVERT: A 58 GLU cc_start: 0.8173 (mp0) cc_final: 0.7913 (mp0) REVERT: D 68 LYS cc_start: 0.8125 (ptpp) cc_final: 0.7896 (ptpp) REVERT: D 118 LYS cc_start: 0.7366 (mtpt) cc_final: 0.6777 (mttm) outliers start: 9 outliers final: 6 residues processed: 112 average time/residue: 0.0890 time to fit residues: 14.1786 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 : 0.238 ------------------------------------------------------------------------------- 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: 3.9990 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.107144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090834 restraints weight = 13562.033| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.95 r_work: 0.2941 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8969 Z= 0.149 Angle : 0.497 7.328 12135 Z= 0.265 Chirality : 0.043 0.192 1352 Planarity : 0.004 0.049 1544 Dihedral : 4.538 46.427 1252 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 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: 0.93 (0.25), residues: 1099 helix: 1.86 (0.23), residues: 543 sheet: 0.03 (0.45), residues: 123 loop : -0.81 (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 0.014 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8968) covalent geometry : angle 0.49718 (12135) hydrogen bonds : bond 0.04568 ( 444) hydrogen bonds : angle 4.18737 ( 1266) Misc. bond : bond 0.00033 ( 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 114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.327 Fit side-chains REVERT: B 89 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8316 (m-30) REVERT: B 456 MET cc_start: 0.8617 (mtm) cc_final: 0.8324 (mtm) REVERT: D 68 LYS cc_start: 0.8156 (ptpp) cc_final: 0.7854 (ptpp) REVERT: D 118 LYS cc_start: 0.7462 (mtpt) cc_final: 0.6877 (mttm) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.0866 time to fit residues: 13.2586 Evaluate side-chains 103 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 58 MET Chi-restraints excluded: chain D residue 114 SER 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: 0.7980 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.107971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091623 restraints weight = 13717.950| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.97 r_work: 0.2950 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1225 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= 0.130 Angle : 0.486 7.196 12135 Z= 0.258 Chirality : 0.042 0.185 1352 Planarity : 0.004 0.046 1544 Dihedral : 4.387 45.655 1252 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 8.67 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.02 (0.23), residues: 541 sheet: 0.05 (0.45), residues: 123 loop : -0.77 (0.27), residues: 435 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 covalent geometry : bond 0.00305 ( 8968) covalent geometry : angle 0.48572 (12135) hydrogen bonds : bond 0.04188 ( 444) hydrogen bonds : angle 4.08048 ( 1266) Misc. bond : bond 0.00037 ( 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 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.356 Fit side-chains REVERT: A 58 GLU cc_start: 0.8077 (mp0) cc_final: 0.7747 (mp0) REVERT: B 89 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: D 68 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7888 (ptpp) REVERT: D 118 LYS cc_start: 0.7472 (mtpt) cc_final: 0.6902 (mttm) outliers start: 16 outliers final: 9 residues processed: 107 average time/residue: 0.0832 time to fit residues: 12.9896 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 : 0.324 ------------------------------------------------------------------------------- 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 1 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.0170 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 = 0.108624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092434 restraints weight = 13473.988| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.94 r_work: 0.2964 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1374 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= 0.119 Angle : 0.469 7.268 12135 Z= 0.249 Chirality : 0.042 0.181 1352 Planarity : 0.004 0.044 1544 Dihedral : 4.267 45.421 1252 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.03 % Allowed : 9.31 % Favored : 88.65 % 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: 1.19 (0.25), residues: 1099 helix: 2.14 (0.23), residues: 536 sheet: 0.05 (0.46), residues: 123 loop : -0.71 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.012 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 covalent geometry : bond 0.00275 ( 8968) covalent geometry : angle 0.46871 (12135) hydrogen bonds : bond 0.03924 ( 444) hydrogen bonds : angle 4.01111 ( 1266) Misc. bond : bond 0.00029 ( 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 125 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.357 Fit side-chains REVERT: B 57 ARG cc_start: 0.8526 (mtm110) cc_final: 0.8325 (mtm-85) REVERT: B 89 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: B 388 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8825 (mt) REVERT: D 118 LYS cc_start: 0.7484 (mtpt) cc_final: 0.6929 (mttm) outliers start: 19 outliers final: 10 residues processed: 114 average time/residue: 0.0935 time to fit residues: 15.0977 Evaluate side-chains 114 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 67 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.0030 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.108751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092353 restraints weight = 13590.703| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.98 r_work: 0.2970 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1452 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= 0.117 Angle : 0.477 7.832 12135 Z= 0.250 Chirality : 0.041 0.179 1352 Planarity : 0.004 0.041 1544 Dihedral : 4.196 44.974 1252 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.03 % Allowed : 9.85 % 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 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: 542 sheet: 0.07 (0.46), residues: 123 loop : -0.70 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.011 0.001 TYR D 26 PHE 0.012 0.001 PHE A 209 TRP 0.011 0.001 TRP C 32 HIS 0.003 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8968) covalent geometry : angle 0.47747 (12135) hydrogen bonds : bond 0.03837 ( 444) hydrogen bonds : angle 3.96995 ( 1266) Misc. bond : bond 0.00025 ( 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 124 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.292 Fit side-chains REVERT: A 58 GLU cc_start: 0.8120 (mp0) cc_final: 0.7837 (mp0) REVERT: B 388 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8828 (mt) REVERT: D 118 LYS cc_start: 0.7499 (mtpt) cc_final: 0.6947 (mttm) REVERT: D 151 ASN cc_start: 0.9234 (t0) cc_final: 0.9029 (t0) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.0871 time to fit residues: 14.2245 Evaluate side-chains 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain B residue 83 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 59 optimal weight: 0.0870 chunk 65 optimal weight: 0.0970 chunk 101 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.123448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107049 restraints weight = 13434.398| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.86 r_work: 0.3185 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1627 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= 0.239 Chirality : 0.041 0.176 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.069 44.934 1252 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.82 % Allowed : 10.49 % 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 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: 2.23 (0.23), residues: 542 sheet: 0.12 (0.47), residues: 123 loop : -0.67 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.011 0.001 TYR D 26 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 covalent geometry : bond 0.00211 ( 8968) covalent geometry : angle 0.45593 (12135) hydrogen bonds : bond 0.03362 ( 444) hydrogen bonds : angle 3.90070 ( 1266) Misc. bond : bond 0.00021 ( 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 122 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.344 Fit side-chains REVERT: A 58 GLU cc_start: 0.8029 (mp0) cc_final: 0.7755 (mp0) REVERT: A 184 ILE cc_start: 0.8730 (mt) cc_final: 0.8489 (tt) REVERT: B 89 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8347 (m-30) REVERT: B 388 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8822 (mt) REVERT: B 529 ASP cc_start: 0.8630 (t0) cc_final: 0.8423 (t0) REVERT: D 118 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7034 (mttm) outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 0.0813 time to fit residues: 13.5270 Evaluate side-chains 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain A residue 326 ASP 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: 0.0980 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 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: 0.8980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.122225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105873 restraints weight = 13476.499| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.85 r_work: 0.3165 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8969 Z= 0.128 Angle : 0.487 9.093 12135 Z= 0.252 Chirality : 0.042 0.178 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.106 44.224 1252 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.61 % Allowed : 11.03 % 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: 1.29 (0.26), residues: 1099 helix: 2.20 (0.23), residues: 542 sheet: 0.13 (0.47), residues: 123 loop : -0.67 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.013 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 covalent geometry : bond 0.00304 ( 8968) covalent geometry : angle 0.48698 (12135) hydrogen bonds : bond 0.03857 ( 444) hydrogen bonds : angle 3.90880 ( 1266) Misc. bond : bond 0.00019 ( 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 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.287 Fit side-chains REVERT: A 58 GLU cc_start: 0.8131 (mp0) cc_final: 0.7881 (mp0) REVERT: B 89 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: B 388 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8817 (mt) REVERT: C 13 MET cc_start: 0.6525 (mmm) cc_final: 0.6217 (mmt) REVERT: D 118 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7026 (mttm) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.0825 time to fit residues: 13.3365 Evaluate side-chains 113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.0370 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS D 13 ASN D 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106567 restraints weight = 13561.689| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.89 r_work: 0.3164 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1594 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 : 0.493 8.533 12135 Z= 0.255 Chirality : 0.042 0.178 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.125 44.469 1252 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.03 % Allowed : 10.71 % 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: 1.28 (0.26), residues: 1099 helix: 2.19 (0.23), residues: 542 sheet: 0.12 (0.46), residues: 123 loop : -0.67 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.010 0.001 TYR D 26 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 covalent geometry : bond 0.00298 ( 8968) covalent geometry : angle 0.49289 (12135) hydrogen bonds : bond 0.03892 ( 444) hydrogen bonds : angle 3.90908 ( 1266) Misc. bond : bond 0.00021 ( 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 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.345 Fit side-chains REVERT: A 58 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 451 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: B 89 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: B 388 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8806 (mt) REVERT: C 13 MET cc_start: 0.6429 (mmm) cc_final: 0.6171 (mmt) REVERT: D 118 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7039 (mttm) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.0873 time to fit residues: 13.6950 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 : 0.324 ------------------------------------------------------------------------------- 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 326 ASP 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 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 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: 2.9990 chunk 98 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.120464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104295 restraints weight = 13224.704| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.85 r_work: 0.3151 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8969 Z= 0.142 Angle : 0.504 8.487 12135 Z= 0.261 Chirality : 0.042 0.178 1352 Planarity : 0.004 0.040 1544 Dihedral : 4.184 44.253 1252 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: 1.22 (0.26), residues: 1099 helix: 2.14 (0.23), residues: 544 sheet: 0.08 (0.46), residues: 123 loop : -0.70 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.010 0.001 TYR D 26 PHE 0.013 0.001 PHE A 209 TRP 0.010 0.001 TRP C 32 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8968) covalent geometry : angle 0.50356 (12135) hydrogen bonds : bond 0.04154 ( 444) hydrogen bonds : angle 3.94201 ( 1266) Misc. bond : bond 0.00019 ( 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 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.358 Fit side-chains REVERT: A 58 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: A 451 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: B 89 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8375 (m-30) REVERT: B 388 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8828 (mt) REVERT: C 13 MET cc_start: 0.6426 (mmm) cc_final: 0.6069 (mmt) REVERT: D 68 LYS cc_start: 0.7841 (pttp) cc_final: 0.7508 (ptpp) REVERT: D 118 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7036 (mttm) outliers start: 17 outliers final: 12 residues processed: 107 average time/residue: 0.0871 time to fit residues: 13.6263 Evaluate side-chains 113 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106542 restraints weight = 13293.565| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.86 r_work: 0.3175 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1689 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= 0.106 Angle : 0.476 8.413 12135 Z= 0.247 Chirality : 0.041 0.175 1352 Planarity : 0.004 0.039 1544 Dihedral : 4.089 44.494 1252 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.82 % Allowed : 11.13 % Favored : 87.04 % 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 (0.26), residues: 1099 helix: 2.28 (0.23), residues: 536 sheet: -0.01 (0.46), residues: 125 loop : -0.65 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 304 TYR 0.010 0.001 TYR D 26 PHE 0.011 0.001 PHE A 209 TRP 0.012 0.001 TRP C 32 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8968) covalent geometry : angle 0.47618 (12135) hydrogen bonds : bond 0.03577 ( 444) hydrogen bonds : angle 3.88677 ( 1266) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.69 seconds wall clock time: 37 minutes 27.00 seconds (2247.00 seconds total)