Starting phenix.real_space_refine on Mon Mar 11 16:03:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbe_34623/03_2024/8hbe_34623_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbe_34623/03_2024/8hbe_34623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbe_34623/03_2024/8hbe_34623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbe_34623/03_2024/8hbe_34623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbe_34623/03_2024/8hbe_34623_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbe_34623/03_2024/8hbe_34623_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.185 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 60 5.16 5 C 5534 2.51 5 N 1457 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A ASP 521": "OD1" <-> "OD2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B ASP 477": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4120 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 542, 4117 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 Conformer: "B" Number of residues, atoms: 542, 4117 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 515} Chain breaks: 5 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 bond proxies already assigned to first conformer: 4196 Chain: "B" Number of atoms: 4490 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 573, 4486 Unusual residues: {'HEM': 1} Classifications: {'peptide': 572, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 548, None: 1} Not linked: pdbres="LYS B 607 " pdbres="HEM B1000 " Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 81 Conformer: "B" Number of residues, atoms: 573, 4486 Unusual residues: {'HEM': 1} Classifications: {'peptide': 572, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 548, None: 1} Not linked: pdbres="LYS B 607 " pdbres="HEM B1000 " Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'GLU:plan': 10, 'ASN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 81 bond proxies already assigned to first conformer: 4579 Time building chain proxies: 8.50, per 1000 atoms: 0.99 Number of scatterers: 8610 At special positions: 0 Unit cell: (75.24, 95.095, 149.435, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 60 16.00 O 1558 8.00 N 1457 7.00 C 5534 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 3.2 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 11 sheets defined 42.7% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 147 Processing helix chain 'A' and resid 159 through 173 removed outlier: 4.900A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.712A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.566A pdb=" N PHE A 393 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 410 through 419 removed outlier: 4.533A pdb=" N GLY A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 427 through 457 removed outlier: 3.525A pdb=" N LYS A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 499 through 520 Processing helix chain 'A' and resid 545 through 562 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'B' and resid 3 through 28 Proline residue: B 19 - end of helix removed outlier: 3.923A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 80 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.679A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 331 through 334 No H-bonds generated for 'chain 'B' and resid 331 through 334' Processing helix chain 'B' and resid 348 through 354 Processing helix chain 'B' and resid 363 through 394 Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 440 through 460 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.317A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLN B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 566 through 572 Processing sheet with id= A, first strand: chain 'A' and resid 189 through 193 removed outlier: 4.060A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.516A pdb=" N THR A 328 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG A 349 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE A 326 " --> pdb=" O ARG A 349 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= D, first strand: chain 'A' and resid 523 through 525 removed outlier: 4.515A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 634 through 636 Processing sheet with id= F, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.642A pdb=" N GLN B 168 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLU B 182 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N MET B 164 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 254 through 258 removed outlier: 6.486A pdb=" N VAL B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP B 224 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.720A pdb=" N LYS B 415 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 529 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 519 through 526 removed outlier: 4.469A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 562 through 564 removed outlier: 4.323A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 603 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 588 through 590 removed outlier: 4.199A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET B 599 " --> pdb=" O VAL B 590 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1211 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: 3.01 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3489 1.38 - 1.56: 5206 1.56 - 1.74: 0 1.74 - 1.92: 93 1.92 - 2.10: 3 Bond restraints: 8791 Sorted by residual: bond pdb=" CA PHE B 359 " pdb=" C PHE B 359 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.28e-02 6.10e+03 1.82e+01 bond pdb=" C3B HEM B1000 " pdb=" CAB HEM B1000 " ideal model delta sigma weight residual 1.544 1.468 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" CA ASN B 329 " pdb=" C ASN B 329 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.31e-02 5.83e+03 1.36e+01 bond pdb=" CA ARG B 360 " pdb=" C ARG B 360 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.42e-02 4.96e+03 1.23e+01 bond pdb=" C3C HEM B1000 " pdb=" CAC HEM B1000 " ideal model delta sigma weight residual 1.544 1.475 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 8786 not shown) Histogram of bond angle deviations from ideal: 85.75 - 101.86: 34 101.86 - 117.96: 6661 117.96 - 134.07: 5238 134.07 - 150.17: 1 150.17 - 166.28: 2 Bond angle restraints: 11936 Sorted by residual: angle pdb=" N PHE B 359 " pdb=" CA PHE B 359 " pdb=" C PHE B 359 " ideal model delta sigma weight residual 112.26 104.89 7.37 1.32e+00 5.74e-01 3.12e+01 angle pdb=" N ALA B 438 " pdb=" CA ALA B 438 " pdb=" C ALA B 438 " ideal model delta sigma weight residual 111.55 117.05 -5.50 1.37e+00 5.33e-01 1.61e+01 angle pdb=" C PRO A 613 " pdb=" N ARG A 614 " pdb=" CA ARG A 614 " ideal model delta sigma weight residual 121.54 128.61 -7.07 1.91e+00 2.74e-01 1.37e+01 angle pdb=" N LYS A 317 " pdb=" CA LYS A 317 " pdb=" C LYS A 317 " ideal model delta sigma weight residual 111.00 119.53 -8.53 2.80e+00 1.28e-01 9.29e+00 angle pdb=" C3D HEM B1000 " pdb=" CAD HEM B1000 " pdb=" CBD HEM B1000 " ideal model delta sigma weight residual 109.50 118.26 -8.76 3.00e+00 1.11e-01 8.52e+00 ... (remaining 11931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 4633 16.65 - 33.30: 464 33.30 - 49.95: 136 49.95 - 66.60: 18 66.60 - 83.25: 15 Dihedral angle restraints: 5266 sinusoidal: 2022 harmonic: 3244 Sorted by residual: dihedral pdb=" C2B HEM B1000 " pdb=" C3B HEM B1000 " pdb=" CAB HEM B1000 " pdb=" CBB HEM B1000 " ideal model delta sinusoidal sigma weight residual 0.00 71.48 -71.48 2 1.00e+01 1.00e-02 4.32e+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 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLY B 35 " pdb=" C GLY B 35 " pdb=" N GLN B 36 " pdb=" CA GLN B 36 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 973 0.044 - 0.087: 298 0.087 - 0.131: 95 0.131 - 0.174: 14 0.174 - 0.218: 6 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA MET B 328 " pdb=" N MET B 328 " pdb=" C MET B 328 " pdb=" CB MET B 328 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA MET B 444 " pdb=" N MET B 444 " pdb=" C MET B 444 " pdb=" CB MET B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1383 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 466 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO B 467 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 467 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 467 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 442 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C GLY B 442 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY B 442 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA B 443 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 258 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 259 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " 0.024 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1286 2.75 - 3.29: 8032 3.29 - 3.83: 14267 3.83 - 4.36: 16833 4.36 - 4.90: 29809 Nonbonded interactions: 70227 Sorted by model distance: nonbonded pdb=" OE1 GLU B 473 " pdb=" NH1 ARG B 539 " model vdw 2.217 2.520 nonbonded pdb=" O LEU B 251 " pdb=" NZ LYS B 281 " model vdw 2.251 2.520 nonbonded pdb=" OH TYR A 510 " pdb=" O GLY A 529 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR A 168 " pdb=" O ASN A 343 " model vdw 2.308 2.440 nonbonded pdb=" NH1 ARG B 121 " pdb=" OH TYR B 136 " model vdw 2.318 2.520 ... (remaining 70222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 0.740 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: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 32.160 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.211 8791 Z= 0.441 Angle : 0.734 16.674 11936 Z= 0.366 Chirality : 0.048 0.218 1386 Planarity : 0.005 0.050 1516 Dihedral : 15.140 83.252 3166 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.20 (0.25), residues: 1097 helix: 0.45 (0.23), residues: 523 sheet: -0.14 (0.32), residues: 247 loop : -0.85 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 602 HIS 0.013 0.001 HIS A 224 PHE 0.017 0.002 PHE B 603 TYR 0.013 0.002 TYR B 135 ARG 0.005 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.887 Fit side-chains REVERT: B 355 LEU cc_start: 0.6425 (mp) cc_final: 0.6218 (mp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2018 time to fit residues: 29.7104 Evaluate side-chains 103 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8791 Z= 0.202 Angle : 0.565 13.500 11936 Z= 0.275 Chirality : 0.042 0.162 1386 Planarity : 0.004 0.040 1516 Dihedral : 5.676 84.177 1200 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.98 % Allowed : 12.31 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.15 (0.25), residues: 1097 helix: 0.78 (0.23), residues: 527 sheet: -0.02 (0.32), residues: 246 loop : -0.72 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 467 HIS 0.010 0.001 HIS A 224 PHE 0.016 0.001 PHE A 141 TYR 0.012 0.001 TYR B 237 ARG 0.003 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: B 599 MET cc_start: 0.6841 (ptp) cc_final: 0.6415 (ptt) outliers start: 9 outliers final: 7 residues processed: 118 average time/residue: 0.2006 time to fit residues: 33.8709 Evaluate side-chains 111 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 475 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8791 Z= 0.226 Angle : 0.561 13.143 11936 Z= 0.273 Chirality : 0.042 0.151 1386 Planarity : 0.004 0.038 1516 Dihedral : 5.624 84.876 1200 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.63 % Allowed : 13.40 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.25 (0.25), residues: 1097 helix: 0.86 (0.23), residues: 527 sheet: 0.02 (0.32), residues: 246 loop : -0.67 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.014 0.001 HIS A 224 PHE 0.016 0.001 PHE A 141 TYR 0.012 0.001 TYR B 237 ARG 0.003 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: B 527 GLU cc_start: 0.6945 (pp20) cc_final: 0.6710 (pp20) REVERT: B 599 MET cc_start: 0.6837 (ptp) cc_final: 0.6408 (ptt) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.1934 time to fit residues: 32.3718 Evaluate side-chains 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 0.0070 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8791 Z= 0.204 Angle : 0.543 12.967 11936 Z= 0.263 Chirality : 0.041 0.151 1386 Planarity : 0.004 0.038 1516 Dihedral : 5.526 86.676 1200 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.96 % Allowed : 13.40 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1097 helix: 1.06 (0.23), residues: 524 sheet: -0.08 (0.31), residues: 256 loop : -0.46 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.003 0.001 HIS A 578 PHE 0.015 0.001 PHE A 141 TYR 0.012 0.001 TYR B 49 ARG 0.003 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7035 (mt) REVERT: A 344 MET cc_start: 0.8544 (mmm) cc_final: 0.8223 (mmt) REVERT: B 384 GLU cc_start: 0.7582 (tp30) cc_final: 0.6871 (tt0) REVERT: B 599 MET cc_start: 0.6728 (ptp) cc_final: 0.6247 (ptt) outliers start: 18 outliers final: 13 residues processed: 125 average time/residue: 0.1947 time to fit residues: 34.8448 Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8791 Z= 0.319 Angle : 0.601 13.683 11936 Z= 0.291 Chirality : 0.043 0.158 1386 Planarity : 0.004 0.039 1516 Dihedral : 5.678 85.698 1200 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.07 % Allowed : 14.60 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.29 (0.25), residues: 1097 helix: 0.93 (0.23), residues: 520 sheet: -0.10 (0.31), residues: 252 loop : -0.58 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 602 HIS 0.004 0.001 HIS A 578 PHE 0.015 0.002 PHE A 141 TYR 0.013 0.001 TYR B 135 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 218 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 366 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8326 (mt) REVERT: B 599 MET cc_start: 0.6749 (ptp) cc_final: 0.6262 (ptt) outliers start: 19 outliers final: 15 residues processed: 124 average time/residue: 0.1914 time to fit residues: 33.8635 Evaluate side-chains 126 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8791 Z= 0.248 Angle : 0.566 13.478 11936 Z= 0.274 Chirality : 0.042 0.148 1386 Planarity : 0.004 0.038 1516 Dihedral : 5.605 87.539 1200 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.07 % Allowed : 14.92 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.35 (0.25), residues: 1097 helix: 0.97 (0.23), residues: 526 sheet: -0.09 (0.31), residues: 251 loop : -0.52 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 602 HIS 0.003 0.001 HIS A 578 PHE 0.015 0.001 PHE A 141 TYR 0.012 0.001 TYR B 237 ARG 0.003 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.035 Fit side-chains REVERT: A 218 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7089 (mt) REVERT: A 344 MET cc_start: 0.8577 (mmm) cc_final: 0.8229 (mmt) REVERT: B 330 LEU cc_start: 0.8767 (tp) cc_final: 0.8378 (mp) REVERT: B 384 GLU cc_start: 0.7590 (tp30) cc_final: 0.6869 (tt0) REVERT: B 599 MET cc_start: 0.6689 (ptp) cc_final: 0.6239 (ptt) outliers start: 19 outliers final: 16 residues processed: 121 average time/residue: 0.1982 time to fit residues: 34.5193 Evaluate side-chains 124 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.0870 chunk 90 optimal weight: 0.0770 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8791 Z= 0.158 Angle : 0.519 11.979 11936 Z= 0.252 Chirality : 0.040 0.140 1386 Planarity : 0.004 0.036 1516 Dihedral : 5.427 88.810 1200 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.63 % Allowed : 15.90 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.67 (0.26), residues: 1097 helix: 1.30 (0.23), residues: 524 sheet: -0.11 (0.31), residues: 256 loop : -0.34 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 467 HIS 0.002 0.001 HIS A 406 PHE 0.015 0.001 PHE A 141 TYR 0.011 0.001 TYR B 237 ARG 0.002 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.8489 (mmm) cc_final: 0.8207 (mmt) REVERT: B 479 TYR cc_start: 0.8477 (t80) cc_final: 0.7638 (t80) REVERT: B 551 SER cc_start: 0.8095 (t) cc_final: 0.7574 (m) REVERT: B 599 MET cc_start: 0.6642 (ptp) cc_final: 0.6188 (ptt) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 0.1933 time to fit residues: 34.8579 Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 563 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8791 Z= 0.179 Angle : 0.528 12.137 11936 Z= 0.257 Chirality : 0.041 0.138 1386 Planarity : 0.004 0.036 1516 Dihedral : 5.418 88.753 1200 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.63 % Allowed : 16.56 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.74 (0.26), residues: 1097 helix: 1.37 (0.23), residues: 524 sheet: -0.07 (0.31), residues: 256 loop : -0.33 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.003 0.001 HIS A 258 PHE 0.014 0.001 PHE A 141 TYR 0.011 0.001 TYR B 237 ARG 0.002 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.8515 (mmm) cc_final: 0.8215 (mmt) REVERT: B 437 HIS cc_start: 0.7084 (m90) cc_final: 0.6815 (m-70) REVERT: B 551 SER cc_start: 0.8125 (t) cc_final: 0.7597 (m) REVERT: B 599 MET cc_start: 0.6638 (ptp) cc_final: 0.6199 (ptt) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.1964 time to fit residues: 33.1231 Evaluate side-chains 119 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 90 optimal weight: 0.0470 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8791 Z= 0.174 Angle : 0.527 12.083 11936 Z= 0.255 Chirality : 0.040 0.137 1386 Planarity : 0.004 0.036 1516 Dihedral : 5.381 88.018 1200 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.53 % Allowed : 16.88 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.83 (0.26), residues: 1097 helix: 1.45 (0.23), residues: 522 sheet: -0.07 (0.31), residues: 256 loop : -0.24 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 602 HIS 0.004 0.001 HIS A 258 PHE 0.014 0.001 PHE A 141 TYR 0.011 0.001 TYR B 237 ARG 0.002 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.8521 (mmm) cc_final: 0.8214 (mmt) REVERT: B 437 HIS cc_start: 0.7071 (m90) cc_final: 0.6821 (m90) REVERT: B 551 SER cc_start: 0.8120 (t) cc_final: 0.7602 (m) REVERT: B 599 MET cc_start: 0.6653 (ptp) cc_final: 0.6241 (ptt) outliers start: 14 outliers final: 13 residues processed: 117 average time/residue: 0.2005 time to fit residues: 33.5640 Evaluate side-chains 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8791 Z= 0.173 Angle : 0.526 12.007 11936 Z= 0.254 Chirality : 0.040 0.136 1386 Planarity : 0.004 0.036 1516 Dihedral : 5.346 87.494 1200 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.63 % Allowed : 16.99 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.90 (0.26), residues: 1097 helix: 1.52 (0.23), residues: 522 sheet: -0.06 (0.31), residues: 256 loop : -0.20 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.003 0.001 HIS A 258 PHE 0.014 0.001 PHE A 141 TYR 0.011 0.001 TYR B 237 ARG 0.002 0.000 ARG B 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 344 MET cc_start: 0.8492 (mmm) cc_final: 0.8190 (mmt) REVERT: B 527 GLU cc_start: 0.6832 (pp20) cc_final: 0.6319 (pt0) REVERT: B 551 SER cc_start: 0.8151 (t) cc_final: 0.7587 (m) REVERT: B 599 MET cc_start: 0.6661 (ptp) cc_final: 0.6220 (ptt) outliers start: 15 outliers final: 15 residues processed: 116 average time/residue: 0.2057 time to fit residues: 34.2963 Evaluate side-chains 119 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 2 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 overall best weight: 0.6544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.167052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.126521 restraints weight = 15170.015| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 4.83 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8791 Z= 0.198 Angle : 0.535 12.402 11936 Z= 0.258 Chirality : 0.041 0.136 1386 Planarity : 0.004 0.037 1516 Dihedral : 5.374 88.171 1200 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.74 % Allowed : 16.99 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.87 (0.26), residues: 1097 helix: 1.48 (0.23), residues: 522 sheet: -0.07 (0.31), residues: 256 loop : -0.19 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.003 0.001 HIS A 258 PHE 0.014 0.001 PHE A 141 TYR 0.011 0.001 TYR B 237 ARG 0.003 0.000 ARG B 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.81 seconds wall clock time: 37 minutes 17.69 seconds (2237.69 seconds total)