Starting phenix.real_space_refine on Fri Dec 8 06:18:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/12_2023/8sda_40350_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/12_2023/8sda_40350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/12_2023/8sda_40350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/12_2023/8sda_40350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/12_2023/8sda_40350_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sda_40350/12_2023/8sda_40350_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 7 5.49 5 S 36 5.16 5 C 4963 2.51 5 N 1117 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7414 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1825 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1823 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1744 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1749 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {' K': 3, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' K': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.11, per 1000 atoms: 0.55 Number of scatterers: 7414 At special positions: 0 Unit cell: (96.28, 96.28, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 36 16.00 P 7 15.00 O 1287 8.00 N 1117 7.00 C 4963 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 172 through 175 No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 182 through 206 removed outlier: 4.047A pdb=" N THR A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 246 removed outlier: 3.682A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 257 through 275 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 289 through 307 removed outlier: 4.519A pdb=" N ILE A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 360 through 372 removed outlier: 4.173A pdb=" N TRP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 427 removed outlier: 3.694A pdb=" N ILE A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 5.018A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 182 through 206 removed outlier: 4.083A pdb=" N THR B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 246 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 257 through 275 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 289 through 307 removed outlier: 4.768A pdb=" N ILE B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ARG B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ALA B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 324 through 348 Processing helix chain 'B' and resid 360 through 371 removed outlier: 4.157A pdb=" N TRP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 Processing helix chain 'B' and resid 405 through 427 removed outlier: 3.735A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 182 through 206 removed outlier: 4.002A pdb=" N THR D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 245 removed outlier: 3.680A pdb=" N ALA D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL D 231 " --> pdb=" O HIS D 227 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N CYS D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 257 through 274 Proline residue: D 268 - end of helix Processing helix chain 'D' and resid 289 through 307 removed outlier: 4.726A pdb=" N ILE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 348 removed outlier: 4.220A pdb=" N ARG D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 371 removed outlier: 4.113A pdb=" N TRP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 426 removed outlier: 3.692A pdb=" N ALA D 402 " --> pdb=" O VAL D 398 " (cutoff:3.500A) Proline residue: D 404 - end of helix removed outlier: 4.368A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 206 removed outlier: 4.126A pdb=" N THR C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 246 removed outlier: 3.858A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.740A pdb=" N ILE C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Proline residue: C 268 - end of helix Processing helix chain 'C' and resid 289 through 307 removed outlier: 4.763A pdb=" N ILE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ARG C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 324 through 348 removed outlier: 3.585A pdb=" N GLY C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 371 removed outlier: 4.116A pdb=" N TRP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 426 Proline residue: C 404 - end of helix removed outlier: 4.594A pdb=" N ILE C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1494 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: 1.98 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1107 1.30 - 1.43: 1874 1.43 - 1.56: 4478 1.56 - 1.68: 26 1.68 - 1.81: 65 Bond restraints: 7550 Sorted by residual: bond pdb=" C21 POV D 602 " pdb=" O21 POV D 602 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" C21 POV A 603 " pdb=" O21 POV A 603 " ideal model delta sigma weight residual 1.330 1.458 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C21 POV A 604 " pdb=" O21 POV A 604 " ideal model delta sigma weight residual 1.330 1.457 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C31 POV A 606 " pdb=" O31 POV A 606 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C21 POV C 603 " pdb=" O21 POV C 603 " ideal model delta sigma weight residual 1.330 1.444 -0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 7545 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 199 106.29 - 113.22: 4315 113.22 - 120.15: 2691 120.15 - 127.08: 2956 127.08 - 134.01: 74 Bond angle restraints: 10235 Sorted by residual: angle pdb=" O13 POV A 601 " pdb=" P POV A 601 " pdb=" O14 POV A 601 " ideal model delta sigma weight residual 121.11 108.34 12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" O11 POV A 602 " pdb=" P POV A 602 " pdb=" O12 POV A 602 " ideal model delta sigma weight residual 97.67 109.76 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" O13 POV B 602 " pdb=" P POV B 602 " pdb=" O14 POV B 602 " ideal model delta sigma weight residual 121.11 109.07 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV D 601 " pdb=" P POV D 601 " pdb=" O12 POV D 601 " ideal model delta sigma weight residual 97.67 109.48 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 POV C 602 " pdb=" P POV C 602 " pdb=" O12 POV C 602 " ideal model delta sigma weight residual 97.67 109.43 -11.76 3.00e+00 1.11e-01 1.54e+01 ... (remaining 10230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 4212 26.14 - 52.27: 221 52.27 - 78.41: 33 78.41 - 104.54: 9 104.54 - 130.68: 1 Dihedral angle restraints: 4476 sinusoidal: 1731 harmonic: 2745 Sorted by residual: dihedral pdb=" C3 POV A 601 " pdb=" C31 POV A 601 " pdb=" O31 POV A 601 " pdb=" C32 POV A 601 " ideal model delta sinusoidal sigma weight residual 172.61 41.93 130.68 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" CB GLU A 239 " pdb=" CG GLU A 239 " pdb=" CD GLU A 239 " pdb=" OE1 GLU A 239 " ideal model delta sinusoidal sigma weight residual 0.00 -83.23 83.23 1 3.00e+01 1.11e-03 9.41e+00 dihedral pdb=" CA GLU B 349 " pdb=" CB GLU B 349 " pdb=" CG GLU B 349 " pdb=" CD GLU B 349 " ideal model delta sinusoidal sigma weight residual 60.00 115.59 -55.59 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 4473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 996 0.051 - 0.103: 215 0.103 - 0.154: 27 0.154 - 0.205: 5 0.205 - 0.257: 2 Chirality restraints: 1245 Sorted by residual: chirality pdb=" CG LEU D 327 " pdb=" CB LEU D 327 " pdb=" CD1 LEU D 327 " pdb=" CD2 LEU D 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA LEU C 225 " pdb=" N LEU C 225 " pdb=" C LEU C 225 " pdb=" CB LEU C 225 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA HIS C 227 " pdb=" N HIS C 227 " pdb=" C HIS C 227 " pdb=" CB HIS C 227 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 1242 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 406 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO B 406 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO B 406 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 407 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 397 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C GLY D 397 " 0.052 2.00e-02 2.50e+03 pdb=" O GLY D 397 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL D 398 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 207 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 208 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.025 5.00e-02 4.00e+02 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.81: 2092 2.81 - 3.39: 9219 3.39 - 3.97: 13953 3.97 - 4.56: 19922 4.56 - 5.14: 27640 Nonbonded interactions: 72826 Sorted by model distance: nonbonded pdb=" O THR B 319 " pdb=" OG SER B 323 " model vdw 2.225 2.440 nonbonded pdb=" O ILE D 407 " pdb=" ND2 ASN D 411 " model vdw 2.280 2.520 nonbonded pdb=" O TYR A 376 " pdb=" K K A 609 " model vdw 2.320 2.850 nonbonded pdb=" O THR C 372 " pdb=" OG1 THR C 373 " model vdw 2.327 2.440 nonbonded pdb=" O THR A 372 " pdb=" OG1 THR A 373 " model vdw 2.355 2.440 ... (remaining 72821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or \ resid 319 through 321 or (resid 322 and (name N or name CA or name C or name O \ or name CB )) or resid 323 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'B' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 211 or resid 224 through 228 or (resid 229 \ through 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 250 or (resid 251 through 252 and (name N or name CA or name C or name \ O or name CB )) or resid 253 through 273 or (resid 274 and (name N or name CA o \ r name C or name O or name CB )) or resid 275 or resid 288 through 308 or (resid \ 309 and (name N or name CA or name C or name O or name CB )) or resid 310 throu \ gh 321 or (resid 322 and (name N or name CA or name C or name O or name CB )) or \ resid 323 through 325 or (resid 326 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 416 or (resid \ 417 and (name N or name CA or name C or name O or name CB )) or resid 418 throu \ gh 419 or (resid 420 through 427 and (name N or name CA or name C or name O or n \ ame CB )))) selection = (chain 'C' and (resid 172 through 211 or resid 224 through 228 or (resid 229 thr \ ough 230 and (name N or name CA or name C or name O or name CB )) or resid 231 t \ hrough 273 or (resid 274 and (name N or name CA or name C or name O or name CB ) \ ) or resid 275 or resid 288 through 409 or (resid 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 427)) selection = (chain 'D' and ((resid 172 through 173 and (name N or name CA or name C or name \ O or name CB )) or resid 174 through 175 or (resid 176 through 177 and (name N o \ r name CA or name C or name O or name CB )) or resid 178 through 308 or (resid 3 \ 09 and (name N or name CA or name C or name O or name CB )) or resid 310 through \ 317 or (resid 318 and (name N or name CA or name C or name O or name CB )) or r \ esid 319 through 427)) } 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: 1.080 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: 6.040 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.110 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 7550 Z= 0.513 Angle : 1.113 12.774 10235 Z= 0.501 Chirality : 0.043 0.257 1245 Planarity : 0.005 0.045 1217 Dihedral : 15.987 130.675 2686 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 1.62 (0.29), residues: 915 helix: 1.30 (0.20), residues: 740 sheet: None (None), residues: 0 loop : 0.42 (0.53), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 172 HIS 0.004 0.001 HIS C 227 PHE 0.011 0.001 PHE A 194 TYR 0.017 0.001 TYR C 416 ARG 0.009 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.894 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2414 time to fit residues: 53.4492 Evaluate side-chains 123 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.0060 chunk 23 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7550 Z= 0.207 Angle : 0.549 7.587 10235 Z= 0.273 Chirality : 0.038 0.137 1245 Planarity : 0.004 0.035 1217 Dihedral : 13.054 110.289 1160 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.17 % Allowed : 10.31 % Favored : 87.52 % 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: 2.55 (0.29), residues: 915 helix: 1.94 (0.20), residues: 748 sheet: None (None), residues: 0 loop : 0.76 (0.52), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 365 HIS 0.003 0.001 HIS B 309 PHE 0.023 0.001 PHE B 415 TYR 0.018 0.001 TYR D 269 ARG 0.005 0.001 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 0.855 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 155 average time/residue: 0.2328 time to fit residues: 46.3421 Evaluate side-chains 135 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0743 time to fit residues: 2.3465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7550 Z= 0.268 Angle : 0.548 8.012 10235 Z= 0.272 Chirality : 0.039 0.133 1245 Planarity : 0.003 0.032 1217 Dihedral : 11.923 101.235 1160 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.17 % Allowed : 13.30 % Favored : 84.53 % 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: 2.62 (0.29), residues: 915 helix: 2.00 (0.20), residues: 746 sheet: None (None), residues: 0 loop : 0.73 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS D 309 PHE 0.025 0.001 PHE B 274 TYR 0.012 0.001 TYR B 269 ARG 0.006 0.001 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 0.850 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 0.2476 time to fit residues: 46.1211 Evaluate side-chains 134 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0722 time to fit residues: 2.5087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7550 Z= 0.219 Angle : 0.526 6.894 10235 Z= 0.261 Chirality : 0.038 0.128 1245 Planarity : 0.003 0.032 1217 Dihedral : 11.314 93.673 1160 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.36 % Allowed : 15.74 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.66 (0.28), residues: 915 helix: 1.99 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.84 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.003 0.000 HIS D 309 PHE 0.019 0.001 PHE B 415 TYR 0.011 0.001 TYR B 269 ARG 0.007 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.795 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 138 average time/residue: 0.2455 time to fit residues: 43.8131 Evaluate side-chains 130 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.845 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0728 time to fit residues: 1.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7550 Z= 0.192 Angle : 0.505 6.834 10235 Z= 0.251 Chirality : 0.037 0.128 1245 Planarity : 0.004 0.048 1217 Dihedral : 10.756 85.497 1160 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.81 % Allowed : 17.10 % Favored : 82.09 % 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: 2.86 (0.28), residues: 915 helix: 2.14 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.86 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.003 0.000 HIS D 309 PHE 0.018 0.001 PHE B 274 TYR 0.010 0.001 TYR B 269 ARG 0.006 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.876 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 140 average time/residue: 0.2531 time to fit residues: 45.2576 Evaluate side-chains 129 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0746 time to fit residues: 1.5812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 chunk 52 optimal weight: 0.0010 chunk 21 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7550 Z= 0.156 Angle : 0.519 9.601 10235 Z= 0.253 Chirality : 0.037 0.125 1245 Planarity : 0.004 0.054 1217 Dihedral : 10.242 84.681 1160 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.54 % Allowed : 18.18 % Favored : 81.28 % 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: 2.99 (0.28), residues: 915 helix: 2.23 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 0.88 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 366 HIS 0.003 0.000 HIS D 309 PHE 0.027 0.001 PHE B 415 TYR 0.009 0.001 TYR B 269 ARG 0.007 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.895 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 137 average time/residue: 0.2436 time to fit residues: 43.3508 Evaluate side-chains 130 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0836 time to fit residues: 1.3331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7550 Z= 0.174 Angle : 0.508 7.943 10235 Z= 0.250 Chirality : 0.037 0.126 1245 Planarity : 0.003 0.030 1217 Dihedral : 9.819 85.381 1160 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.41 % Allowed : 19.27 % Favored : 80.33 % 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: 3.09 (0.28), residues: 915 helix: 2.27 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 1.11 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.003 0.000 HIS D 309 PHE 0.023 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.008 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 0.837 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 134 average time/residue: 0.2466 time to fit residues: 42.7173 Evaluate side-chains 127 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0868 time to fit residues: 1.2619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7550 Z= 0.189 Angle : 0.530 9.658 10235 Z= 0.261 Chirality : 0.038 0.135 1245 Planarity : 0.003 0.031 1217 Dihedral : 9.540 85.664 1160 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.95 % Allowed : 18.59 % Favored : 80.46 % 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: 3.12 (0.28), residues: 915 helix: 2.29 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 1.11 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS D 309 PHE 0.023 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.008 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.863 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 134 average time/residue: 0.2471 time to fit residues: 42.6693 Evaluate side-chains 131 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0709 time to fit residues: 1.7125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7550 Z= 0.197 Angle : 0.529 8.489 10235 Z= 0.262 Chirality : 0.038 0.136 1245 Planarity : 0.003 0.034 1217 Dihedral : 9.265 85.858 1160 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.41 % Allowed : 19.27 % Favored : 80.33 % 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: 3.13 (0.29), residues: 915 helix: 2.29 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 1.11 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.008 0.001 HIS B 309 PHE 0.025 0.001 PHE B 274 TYR 0.010 0.001 TYR B 269 ARG 0.009 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 132 average time/residue: 0.2434 time to fit residues: 41.3312 Evaluate side-chains 121 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0653 time to fit residues: 1.1347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 56 optimal weight: 0.0370 chunk 44 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7550 Z= 0.166 Angle : 0.561 12.741 10235 Z= 0.271 Chirality : 0.037 0.145 1245 Planarity : 0.005 0.087 1217 Dihedral : 8.933 86.955 1160 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.27 % Allowed : 20.08 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.16 (0.28), residues: 915 helix: 2.31 (0.19), residues: 758 sheet: None (None), residues: 0 loop : 1.13 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 366 HIS 0.002 0.000 HIS B 309 PHE 0.025 0.001 PHE B 274 TYR 0.009 0.001 TYR B 269 ARG 0.011 0.001 ARG D 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.2456 time to fit residues: 42.9693 Evaluate side-chains 125 residues out of total 823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 64 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121960 restraints weight = 9999.920| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.02 r_work: 0.3298 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7550 Z= 0.169 Angle : 0.567 11.217 10235 Z= 0.272 Chirality : 0.038 0.158 1245 Planarity : 0.004 0.065 1217 Dihedral : 8.781 87.347 1160 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.14 % Allowed : 20.35 % Favored : 79.51 % 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: 3.21 (0.29), residues: 915 helix: 2.34 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 1.17 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 366 HIS 0.004 0.001 HIS B 309 PHE 0.040 0.001 PHE B 415 TYR 0.009 0.001 TYR B 269 ARG 0.009 0.001 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2015.54 seconds wall clock time: 37 minutes 13.63 seconds (2233.63 seconds total)