Starting phenix.real_space_refine on Tue Sep 24 17:16:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/09_2024/6jt2_9885.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/09_2024/6jt2_9885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/09_2024/6jt2_9885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/09_2024/6jt2_9885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/09_2024/6jt2_9885.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/09_2024/6jt2_9885.cif" } resolution = 3.8 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= 0.004 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8191 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3742 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 8 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 4372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 4452 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 Time building chain proxies: 7.42, per 1000 atoms: 0.91 Number of scatterers: 8191 At special positions: 0 Unit cell: (147.345, 87.78, 98.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 56 16.00 P 3 15.00 Mg 2 11.99 O 1475 8.00 N 1392 7.00 C 5262 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=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.4 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 50.4% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 149 removed outlier: 3.585A pdb=" N ILE A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.375A pdb=" N VAL A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.800A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 4.660A pdb=" N LEU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.643A pdb=" N LYS A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 408 through 458 removed outlier: 4.206A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 4.336A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 removed outlier: 3.508A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.517A pdb=" N GLN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 561 removed outlier: 3.649A pdb=" N GLN A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.642A pdb=" N ASN A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 628 removed outlier: 4.133A pdb=" N ASP A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 18 removed outlier: 4.201A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 removed outlier: 3.931A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.803A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 83 through 90 removed outlier: 3.938A pdb=" N LEU B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 removed outlier: 4.732A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.206A pdb=" N ILE B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.692A pdb=" N VAL B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 253' Processing helix chain 'B' and resid 264 through 271 removed outlier: 3.892A pdb=" N SER B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 285 removed outlier: 4.350A pdb=" N LEU B 285 " --> pdb=" O GLU B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.575A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 348 through 398 removed outlier: 4.370A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 removed outlier: 4.384A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 443 through 461 Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.532A pdb=" N SER B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.641A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 204 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.563A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525 removed outlier: 4.409A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LYS A 476 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ALA A 584 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N SER A 478 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL A 582 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N MET A 573 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ASN A 617 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 575 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 657 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 124 Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.692A pdb=" N GLN B 231 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 415 through 416 removed outlier: 3.532A pdb=" N GLY B 531 " --> pdb=" O CYS B 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 469 through 474 removed outlier: 7.068A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 474 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASN B 563 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 512 461 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3335 1.39 - 1.56: 4924 1.56 - 1.73: 6 1.73 - 1.90: 86 1.90 - 2.07: 4 Bond restraints: 8355 Sorted by residual: bond pdb=" O3B G2P A1001 " pdb=" PG G2P A1001 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O1A G2P A1001 " pdb=" PA G2P A1001 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O1B G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C4 G2P A1001 " pdb=" C5 G2P A1001 " ideal model delta sigma weight residual 1.384 1.469 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 G2P A1001 " pdb=" C6 G2P A1001 " ideal model delta sigma weight residual 1.420 1.483 -0.063 2.00e-02 2.50e+03 9.79e+00 ... (remaining 8350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 11160 2.27 - 4.54: 170 4.54 - 6.81: 22 6.81 - 9.09: 11 9.09 - 11.36: 4 Bond angle restraints: 11367 Sorted by residual: angle pdb=" PA G2P A1001 " pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 120.83 109.47 11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " pdb=" O3B G2P A1001 " ideal model delta sigma weight residual 99.71 109.82 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C5 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N3 G2P A1001 " ideal model delta sigma weight residual 128.08 118.69 9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.28e+00 angle pdb=" C3A G2P A1001 " pdb=" PA G2P A1001 " pdb=" O5' G2P A1001 " ideal model delta sigma weight residual 99.14 108.27 -9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 11362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 4668 16.26 - 32.52: 249 32.52 - 48.78: 56 48.78 - 65.03: 15 65.03 - 81.29: 4 Dihedral angle restraints: 4992 sinusoidal: 1869 harmonic: 3123 Sorted by residual: dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR B 339 " pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta harmonic sigma weight residual 180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE A 301 " pdb=" C PHE A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1106 0.055 - 0.111: 213 0.111 - 0.166: 22 0.166 - 0.221: 0 0.221 - 0.276: 1 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL A 462 " pdb=" CA VAL A 462 " pdb=" CG1 VAL A 462 " pdb=" CG2 VAL A 462 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA VAL A 462 " pdb=" N VAL A 462 " pdb=" C VAL A 462 " pdb=" CB VAL A 462 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C2' G2P A1001 " pdb=" C1' G2P A1001 " pdb=" C3' G2P A1001 " pdb=" O2' G2P A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1339 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C VAL A 462 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 462 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 463 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 258 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO B 259 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 209 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 210 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.031 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 47 2.56 - 3.15: 6531 3.15 - 3.73: 12626 3.73 - 4.32: 16476 4.32 - 4.90: 27806 Nonbonded interactions: 63486 Sorted by model distance: nonbonded pdb=" O2B G2P A1001 " pdb="MG MG A1002 " model vdw 1.980 2.170 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1002 " model vdw 2.095 2.170 nonbonded pdb=" OD2 ASP A 486 " pdb="MG MG A1002 " model vdw 2.101 2.170 nonbonded pdb=" O5' G2P A1001 " pdb="MG MG A1003 " model vdw 2.172 2.170 nonbonded pdb=" O LEU A 520 " pdb=" NE2 GLN A 548 " model vdw 2.259 3.120 ... (remaining 63481 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.790 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.240 Find NCS groups from input model: 0.110 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.004 0.106 8355 Z= 0.283 Angle : 0.738 11.357 11367 Z= 0.377 Chirality : 0.042 0.276 1342 Planarity : 0.005 0.058 1431 Dihedral : 11.363 81.292 2966 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.00 % Favored : 95.71 % Rotamer: Outliers : 3.54 % Allowed : 5.19 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.54 (0.23), residues: 1049 helix: -1.24 (0.20), residues: 478 sheet: -1.17 (0.35), residues: 192 loop : -2.34 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.005 0.001 HIS B 105 PHE 0.016 0.002 PHE A 292 TYR 0.013 0.001 TYR B 479 ARG 0.003 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 CYS cc_start: 0.8998 (t) cc_final: 0.8778 (m) REVERT: A 455 CYS cc_start: 0.8971 (m) cc_final: 0.8406 (t) REVERT: A 479 ASN cc_start: 0.7920 (m110) cc_final: 0.7647 (p0) REVERT: A 514 ASP cc_start: 0.9019 (m-30) cc_final: 0.8740 (m-30) REVERT: A 516 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8498 (mm-40) REVERT: A 543 ASP cc_start: 0.8435 (m-30) cc_final: 0.7491 (p0) REVERT: A 554 VAL cc_start: 0.9375 (t) cc_final: 0.9168 (t) REVERT: A 556 MET cc_start: 0.9443 (tpp) cc_final: 0.8926 (mmm) REVERT: A 583 PHE cc_start: 0.8186 (m-80) cc_final: 0.7859 (m-10) REVERT: B 73 MET cc_start: 0.8564 (tpp) cc_final: 0.8300 (tpp) REVERT: B 106 ASP cc_start: 0.9202 (t0) cc_final: 0.8917 (t0) REVERT: B 119 SER cc_start: 0.9177 (m) cc_final: 0.8363 (p) REVERT: B 160 THR cc_start: 0.8562 (m) cc_final: 0.8351 (p) REVERT: B 211 TYR cc_start: 0.8649 (t80) cc_final: 0.8372 (t80) REVERT: B 228 VAL cc_start: 0.8802 (t) cc_final: 0.8571 (p) REVERT: B 320 LEU cc_start: 0.8545 (tt) cc_final: 0.8089 (tp) REVERT: B 323 CYS cc_start: 0.8540 (p) cc_final: 0.8244 (p) REVERT: B 394 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 491 HIS cc_start: 0.8482 (p90) cc_final: 0.7513 (t-170) REVERT: B 537 MET cc_start: 0.8659 (ttm) cc_final: 0.8425 (ttt) outliers start: 30 outliers final: 11 residues processed: 212 average time/residue: 0.1909 time to fit residues: 55.4702 Evaluate side-chains 123 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 408 HIS B 548 ASN B 563 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8355 Z= 0.205 Angle : 0.695 10.251 11367 Z= 0.348 Chirality : 0.043 0.191 1342 Planarity : 0.005 0.047 1431 Dihedral : 7.828 69.584 1203 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.01 % Allowed : 12.63 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.02 (0.25), residues: 1049 helix: 0.43 (0.22), residues: 487 sheet: -0.91 (0.35), residues: 207 loop : -2.00 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 467 HIS 0.010 0.001 HIS B 266 PHE 0.024 0.002 PHE A 335 TYR 0.025 0.002 TYR B 237 ARG 0.008 0.001 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6283 (t80) REVERT: A 341 MET cc_start: 0.7827 (tpt) cc_final: 0.7577 (tpp) REVERT: A 455 CYS cc_start: 0.9117 (m) cc_final: 0.8357 (t) REVERT: A 479 ASN cc_start: 0.7826 (m110) cc_final: 0.7370 (p0) REVERT: A 511 THR cc_start: 0.9394 (p) cc_final: 0.8996 (t) REVERT: A 514 ASP cc_start: 0.9028 (m-30) cc_final: 0.8746 (m-30) REVERT: A 515 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: A 516 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8611 (mm-40) REVERT: A 543 ASP cc_start: 0.8480 (m-30) cc_final: 0.7533 (p0) REVERT: A 556 MET cc_start: 0.9348 (tpp) cc_final: 0.9077 (mmm) REVERT: A 583 PHE cc_start: 0.8308 (m-80) cc_final: 0.7972 (m-10) REVERT: B 73 MET cc_start: 0.8639 (tpp) cc_final: 0.8335 (tpp) REVERT: B 106 ASP cc_start: 0.9189 (t0) cc_final: 0.8843 (t0) REVERT: B 119 SER cc_start: 0.9178 (m) cc_final: 0.8266 (p) REVERT: B 320 LEU cc_start: 0.8535 (tt) cc_final: 0.8285 (tp) REVERT: B 375 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8223 (ttm170) REVERT: B 491 HIS cc_start: 0.8411 (p90) cc_final: 0.7526 (t-170) REVERT: B 537 MET cc_start: 0.8667 (ttm) cc_final: 0.8278 (ttt) outliers start: 34 outliers final: 21 residues processed: 144 average time/residue: 0.1653 time to fit residues: 34.8175 Evaluate side-chains 129 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 0.0050 chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 ASN B 266 HIS B 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8355 Z= 0.176 Angle : 0.642 8.745 11367 Z= 0.320 Chirality : 0.042 0.275 1342 Planarity : 0.004 0.046 1431 Dihedral : 7.434 70.721 1198 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.66 % Allowed : 14.40 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1049 helix: 0.90 (0.22), residues: 489 sheet: -0.46 (0.37), residues: 196 loop : -1.97 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 22 HIS 0.012 0.001 HIS B 266 PHE 0.018 0.002 PHE B 433 TYR 0.013 0.001 TYR B 569 ARG 0.005 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6266 (t80) REVERT: A 455 CYS cc_start: 0.8988 (m) cc_final: 0.8342 (t) REVERT: A 479 ASN cc_start: 0.7815 (m110) cc_final: 0.7408 (p0) REVERT: A 511 THR cc_start: 0.9345 (p) cc_final: 0.9069 (t) REVERT: A 514 ASP cc_start: 0.8988 (m-30) cc_final: 0.8576 (m-30) REVERT: A 515 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: A 516 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8570 (tp-100) REVERT: A 543 ASP cc_start: 0.8535 (m-30) cc_final: 0.7601 (p0) REVERT: A 573 MET cc_start: 0.9055 (tpt) cc_final: 0.8717 (tpt) REVERT: A 583 PHE cc_start: 0.8366 (m-80) cc_final: 0.8029 (m-10) REVERT: B 1 MET cc_start: 0.8530 (tpp) cc_final: 0.8183 (ttm) REVERT: B 73 MET cc_start: 0.8669 (tpp) cc_final: 0.8364 (tpp) REVERT: B 106 ASP cc_start: 0.9189 (t0) cc_final: 0.8835 (t0) REVERT: B 119 SER cc_start: 0.9180 (m) cc_final: 0.8343 (p) REVERT: B 320 LEU cc_start: 0.8600 (tt) cc_final: 0.8398 (tp) REVERT: B 375 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8336 (ttm170) REVERT: B 491 HIS cc_start: 0.8419 (p90) cc_final: 0.7515 (t-170) REVERT: B 503 MET cc_start: 0.9183 (mtp) cc_final: 0.8730 (mmm) REVERT: B 537 MET cc_start: 0.8650 (ttm) cc_final: 0.8295 (ttt) outliers start: 31 outliers final: 17 residues processed: 145 average time/residue: 0.1549 time to fit residues: 33.3143 Evaluate side-chains 125 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 408 HIS B 451 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8355 Z= 0.174 Angle : 0.615 9.728 11367 Z= 0.303 Chirality : 0.041 0.188 1342 Planarity : 0.004 0.044 1431 Dihedral : 6.585 69.987 1194 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.31 % Allowed : 15.23 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1049 helix: 1.23 (0.23), residues: 493 sheet: -0.52 (0.36), residues: 205 loop : -1.78 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 22 HIS 0.003 0.001 HIS A 406 PHE 0.022 0.002 PHE A 141 TYR 0.013 0.001 TYR B 237 ARG 0.005 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6445 (t80) REVERT: A 455 CYS cc_start: 0.9003 (m) cc_final: 0.8352 (t) REVERT: A 479 ASN cc_start: 0.7713 (m110) cc_final: 0.7160 (p0) REVERT: A 515 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: A 516 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8557 (tp-100) REVERT: A 543 ASP cc_start: 0.8561 (m-30) cc_final: 0.7613 (p0) REVERT: A 573 MET cc_start: 0.9113 (tpt) cc_final: 0.8775 (tpt) REVERT: A 583 PHE cc_start: 0.8385 (m-80) cc_final: 0.8096 (m-10) REVERT: A 607 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 1 MET cc_start: 0.8721 (tpp) cc_final: 0.8469 (ttm) REVERT: B 61 LEU cc_start: 0.8494 (pt) cc_final: 0.8285 (tt) REVERT: B 73 MET cc_start: 0.8698 (tpp) cc_final: 0.8401 (tpp) REVERT: B 106 ASP cc_start: 0.9209 (t0) cc_final: 0.8852 (t0) REVERT: B 119 SER cc_start: 0.9205 (m) cc_final: 0.8343 (p) REVERT: B 375 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8329 (ttm170) REVERT: B 491 HIS cc_start: 0.8493 (p90) cc_final: 0.7546 (t-170) REVERT: B 498 HIS cc_start: 0.9053 (m90) cc_final: 0.8755 (m-70) REVERT: B 503 MET cc_start: 0.9213 (mtp) cc_final: 0.8747 (mmm) outliers start: 28 outliers final: 18 residues processed: 138 average time/residue: 0.1823 time to fit residues: 37.4410 Evaluate side-chains 123 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 515 GLN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8355 Z= 0.189 Angle : 0.599 9.769 11367 Z= 0.295 Chirality : 0.041 0.165 1342 Planarity : 0.004 0.044 1431 Dihedral : 6.535 68.415 1194 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.84 % Allowed : 15.35 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1049 helix: 1.35 (0.23), residues: 494 sheet: -0.36 (0.37), residues: 200 loop : -1.73 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 22 HIS 0.004 0.001 HIS A 406 PHE 0.018 0.002 PHE B 433 TYR 0.012 0.001 TYR B 479 ARG 0.004 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 107 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 291 MET cc_start: 0.8455 (mtp) cc_final: 0.8037 (mtp) REVERT: A 341 MET cc_start: 0.8281 (mmm) cc_final: 0.7619 (tpt) REVERT: A 479 ASN cc_start: 0.7799 (m110) cc_final: 0.7232 (p0) REVERT: A 516 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8561 (tp-100) REVERT: A 543 ASP cc_start: 0.8612 (m-30) cc_final: 0.7655 (p0) REVERT: A 556 MET cc_start: 0.9315 (tpp) cc_final: 0.8896 (mmm) REVERT: A 573 MET cc_start: 0.9150 (tpt) cc_final: 0.8869 (tpt) REVERT: A 583 PHE cc_start: 0.8444 (m-80) cc_final: 0.8144 (m-10) REVERT: A 607 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7814 (t80) REVERT: B 73 MET cc_start: 0.8751 (tpp) cc_final: 0.8440 (tpp) REVERT: B 106 ASP cc_start: 0.9230 (t0) cc_final: 0.8842 (t0) REVERT: B 124 ASP cc_start: 0.8713 (m-30) cc_final: 0.8306 (t0) REVERT: B 375 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8320 (ttm170) REVERT: B 491 HIS cc_start: 0.8513 (p90) cc_final: 0.7562 (t-170) REVERT: B 503 MET cc_start: 0.9274 (mtp) cc_final: 0.8672 (mmm) outliers start: 41 outliers final: 25 residues processed: 142 average time/residue: 0.1597 time to fit residues: 33.1759 Evaluate side-chains 125 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 408 HIS B 563 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8355 Z= 0.181 Angle : 0.594 9.306 11367 Z= 0.292 Chirality : 0.041 0.273 1342 Planarity : 0.004 0.047 1431 Dihedral : 6.501 66.667 1194 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.37 % Allowed : 16.17 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1049 helix: 1.41 (0.23), residues: 492 sheet: -0.29 (0.36), residues: 210 loop : -1.60 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 22 HIS 0.004 0.001 HIS A 406 PHE 0.016 0.001 PHE A 141 TYR 0.012 0.001 TYR B 237 ARG 0.004 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6465 (t80) REVERT: A 291 MET cc_start: 0.8429 (mtp) cc_final: 0.8014 (mtp) REVERT: A 341 MET cc_start: 0.8235 (mmm) cc_final: 0.7597 (tpt) REVERT: A 479 ASN cc_start: 0.7593 (m110) cc_final: 0.7072 (p0) REVERT: A 516 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8562 (tp-100) REVERT: A 543 ASP cc_start: 0.8589 (m-30) cc_final: 0.7622 (p0) REVERT: A 573 MET cc_start: 0.9154 (tpt) cc_final: 0.8912 (tpt) REVERT: A 583 PHE cc_start: 0.8481 (m-80) cc_final: 0.8197 (m-10) REVERT: A 607 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7789 (t80) REVERT: B 73 MET cc_start: 0.8847 (tpp) cc_final: 0.8492 (tpp) REVERT: B 106 ASP cc_start: 0.9216 (t0) cc_final: 0.8801 (t0) REVERT: B 124 ASP cc_start: 0.8703 (m-30) cc_final: 0.8321 (t0) REVERT: B 375 ARG cc_start: 0.8594 (ttp80) cc_final: 0.8289 (ttm170) REVERT: B 491 HIS cc_start: 0.8532 (p90) cc_final: 0.7576 (t-170) REVERT: B 503 MET cc_start: 0.9314 (mtp) cc_final: 0.8705 (mmm) outliers start: 37 outliers final: 27 residues processed: 130 average time/residue: 0.1618 time to fit residues: 31.0286 Evaluate side-chains 129 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.0070 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN B 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8355 Z= 0.180 Angle : 0.598 10.824 11367 Z= 0.290 Chirality : 0.041 0.249 1342 Planarity : 0.004 0.048 1431 Dihedral : 6.493 66.067 1193 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.01 % Allowed : 16.77 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1049 helix: 1.41 (0.23), residues: 493 sheet: -0.29 (0.37), residues: 213 loop : -1.54 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 22 HIS 0.004 0.001 HIS A 406 PHE 0.015 0.001 PHE A 141 TYR 0.013 0.001 TYR B 237 ARG 0.003 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6436 (t80) REVERT: A 291 MET cc_start: 0.8395 (mtp) cc_final: 0.7969 (mtp) REVERT: A 341 MET cc_start: 0.8138 (mmm) cc_final: 0.7555 (tpt) REVERT: A 399 TYR cc_start: 0.7883 (m-80) cc_final: 0.7369 (m-80) REVERT: A 479 ASN cc_start: 0.7536 (m110) cc_final: 0.7014 (p0) REVERT: A 543 ASP cc_start: 0.8591 (m-30) cc_final: 0.7667 (p0) REVERT: A 583 PHE cc_start: 0.8561 (m-80) cc_final: 0.8231 (m-10) REVERT: A 607 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7744 (t80) REVERT: B 73 MET cc_start: 0.8898 (tpp) cc_final: 0.8562 (tpp) REVERT: B 106 ASP cc_start: 0.9235 (t0) cc_final: 0.8941 (t0) REVERT: B 124 ASP cc_start: 0.8697 (m-30) cc_final: 0.8320 (t0) REVERT: B 375 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8281 (ttm170) REVERT: B 491 HIS cc_start: 0.8529 (p90) cc_final: 0.7558 (t-170) REVERT: B 503 MET cc_start: 0.9351 (mtp) cc_final: 0.9133 (mtp) outliers start: 34 outliers final: 24 residues processed: 134 average time/residue: 0.1552 time to fit residues: 30.8313 Evaluate side-chains 119 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.0980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8355 Z= 0.178 Angle : 0.602 10.966 11367 Z= 0.292 Chirality : 0.041 0.228 1342 Planarity : 0.004 0.050 1431 Dihedral : 6.405 64.974 1191 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.13 % Allowed : 16.88 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1049 helix: 1.48 (0.23), residues: 494 sheet: -0.10 (0.37), residues: 213 loop : -1.47 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 22 HIS 0.004 0.001 HIS A 406 PHE 0.014 0.002 PHE A 458 TYR 0.013 0.001 TYR B 339 ARG 0.003 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.6468 (t80) REVERT: A 291 MET cc_start: 0.8345 (mtp) cc_final: 0.7954 (mtp) REVERT: A 341 MET cc_start: 0.8068 (mmm) cc_final: 0.7533 (tpt) REVERT: A 364 MET cc_start: 0.8320 (ttp) cc_final: 0.8099 (ttp) REVERT: A 399 TYR cc_start: 0.7952 (m-80) cc_final: 0.7445 (m-80) REVERT: A 479 ASN cc_start: 0.7522 (m110) cc_final: 0.7005 (p0) REVERT: A 543 ASP cc_start: 0.8616 (m-30) cc_final: 0.7688 (p0) REVERT: A 573 MET cc_start: 0.9173 (tpt) cc_final: 0.8815 (tpt) REVERT: A 607 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 73 MET cc_start: 0.8898 (tpp) cc_final: 0.8564 (tpp) REVERT: B 106 ASP cc_start: 0.9286 (t0) cc_final: 0.8913 (t0) REVERT: B 124 ASP cc_start: 0.8695 (m-30) cc_final: 0.8328 (t0) REVERT: B 375 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8298 (ttm170) REVERT: B 491 HIS cc_start: 0.8619 (p90) cc_final: 0.7713 (t-170) REVERT: B 503 MET cc_start: 0.9376 (mtp) cc_final: 0.9166 (mtp) outliers start: 35 outliers final: 24 residues processed: 128 average time/residue: 0.1662 time to fit residues: 31.2863 Evaluate side-chains 121 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8355 Z= 0.174 Angle : 0.604 11.859 11367 Z= 0.292 Chirality : 0.041 0.230 1342 Planarity : 0.004 0.051 1431 Dihedral : 6.298 64.728 1191 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.42 % Allowed : 17.00 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1049 helix: 1.60 (0.23), residues: 494 sheet: -0.06 (0.37), residues: 217 loop : -1.43 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 22 HIS 0.013 0.001 HIS B 498 PHE 0.014 0.001 PHE B 321 TYR 0.014 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6491 (t80) REVERT: A 291 MET cc_start: 0.8239 (mtp) cc_final: 0.7857 (mtp) REVERT: A 341 MET cc_start: 0.8058 (mmm) cc_final: 0.7792 (tpt) REVERT: A 364 MET cc_start: 0.8289 (ttp) cc_final: 0.8059 (ttp) REVERT: A 399 TYR cc_start: 0.7934 (m-80) cc_final: 0.7390 (m-80) REVERT: A 479 ASN cc_start: 0.7542 (m110) cc_final: 0.7041 (p0) REVERT: A 543 ASP cc_start: 0.8629 (m-30) cc_final: 0.7709 (p0) REVERT: A 573 MET cc_start: 0.9243 (tpt) cc_final: 0.8854 (tpt) REVERT: A 583 PHE cc_start: 0.8412 (m-80) cc_final: 0.7946 (m-10) REVERT: A 607 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7702 (t80) REVERT: B 73 MET cc_start: 0.8886 (tpp) cc_final: 0.8536 (tpp) REVERT: B 106 ASP cc_start: 0.9301 (t0) cc_final: 0.8932 (t0) REVERT: B 124 ASP cc_start: 0.8695 (m-30) cc_final: 0.8340 (t0) REVERT: B 375 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8305 (ttm170) REVERT: B 491 HIS cc_start: 0.8533 (p90) cc_final: 0.7702 (t-170) outliers start: 29 outliers final: 25 residues processed: 121 average time/residue: 0.1581 time to fit residues: 28.2523 Evaluate side-chains 121 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.0000 chunk 105 optimal weight: 0.0070 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8355 Z= 0.149 Angle : 0.612 12.709 11367 Z= 0.296 Chirality : 0.041 0.203 1342 Planarity : 0.004 0.051 1431 Dihedral : 6.189 67.748 1191 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 18.42 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1049 helix: 1.63 (0.23), residues: 494 sheet: 0.06 (0.37), residues: 217 loop : -1.45 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 22 HIS 0.014 0.001 HIS B 498 PHE 0.014 0.001 PHE B 321 TYR 0.016 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 291 MET cc_start: 0.8117 (mtp) cc_final: 0.7734 (mtp) REVERT: A 341 MET cc_start: 0.8003 (mmm) cc_final: 0.7479 (tpt) REVERT: A 364 MET cc_start: 0.8212 (ttp) cc_final: 0.7949 (ttp) REVERT: A 479 ASN cc_start: 0.7533 (m110) cc_final: 0.7021 (p0) REVERT: A 513 PHE cc_start: 0.8793 (m-10) cc_final: 0.8571 (m-80) REVERT: A 543 ASP cc_start: 0.8614 (m-30) cc_final: 0.7708 (p0) REVERT: A 573 MET cc_start: 0.9247 (tpt) cc_final: 0.8844 (tpt) REVERT: A 583 PHE cc_start: 0.8427 (m-80) cc_final: 0.7786 (m-10) REVERT: A 607 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 73 MET cc_start: 0.8854 (tpp) cc_final: 0.8515 (tpp) REVERT: B 124 ASP cc_start: 0.8669 (m-30) cc_final: 0.8354 (t0) REVERT: B 375 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8295 (ttm170) REVERT: B 444 MET cc_start: 0.8649 (tpt) cc_final: 0.8156 (mpp) REVERT: B 491 HIS cc_start: 0.8530 (p90) cc_final: 0.7693 (t-170) outliers start: 21 outliers final: 18 residues processed: 121 average time/residue: 0.1632 time to fit residues: 28.9743 Evaluate side-chains 113 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.106206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084675 restraints weight = 22490.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085646 restraints weight = 13943.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086499 restraints weight = 12275.325| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8355 Z= 0.190 Angle : 0.623 12.411 11367 Z= 0.301 Chirality : 0.041 0.171 1342 Planarity : 0.004 0.047 1431 Dihedral : 6.106 63.351 1190 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.83 % Allowed : 17.95 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 1049 helix: 1.65 (0.23), residues: 494 sheet: 0.13 (0.37), residues: 217 loop : -1.37 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 22 HIS 0.013 0.001 HIS B 498 PHE 0.015 0.002 PHE B 321 TYR 0.014 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.41 seconds wall clock time: 33 minutes 39.16 seconds (2019.16 seconds total)