Starting phenix.real_space_refine on Sat Aug 3 23:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvu_34138/08_2024/7yvu_34138.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvu_34138/08_2024/7yvu_34138.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/7yvu_34138/08_2024/7yvu_34138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvu_34138/08_2024/7yvu_34138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvu_34138/08_2024/7yvu_34138.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvu_34138/08_2024/7yvu_34138.cif" } 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3164 atoms to isotropic. 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 Zn 1 6.06 5 S 37 5.16 5 C 4124 2.51 5 N 1081 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4856 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1557 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.84, per 1000 atoms: 0.90 Number of scatterers: 6456 At special positions: 0 Unit cell: (81.07, 90.45, 114.57, 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) Zn 1 29.99 S 37 16.00 O 1213 8.00 N 1081 7.00 C 4124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 546 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 378 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 57.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 52 removed outlier: 4.352A pdb=" N ASN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.571A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.597A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.842A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.741A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.713A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.656A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.397A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 283 Proline residue: A 280 - end of helix removed outlier: 4.109A pdb=" N VAL A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.580A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.591A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.521A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.839A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.549A pdb=" N ALA A 501 " --> pdb=" O CYS A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.571A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.594A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.078A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.810A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 570 " --> pdb=" O TRP A 566 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.608A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.629A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.711A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.041A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.681A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.277A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.059A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 284 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.48: 1820 1.48 - 1.61: 2680 1.61 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 6638 Sorted by residual: bond pdb=" CA ASN A 49 " pdb=" C ASN A 49 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.35e-02 5.49e+03 8.43e+00 bond pdb=" N GLU A 402 " pdb=" CA GLU A 402 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.96e+00 bond pdb=" CB PRO B 521 " pdb=" CG PRO B 521 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.41e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.859 -0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 6633 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 206 106.99 - 113.75: 3498 113.75 - 120.51: 2746 120.51 - 127.27: 2478 127.27 - 134.03: 90 Bond angle restraints: 9018 Sorted by residual: angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 113.20 108.38 4.82 9.60e-01 1.09e+00 2.52e+01 angle pdb=" C ASP A 509 " pdb=" CA ASP A 509 " pdb=" CB ASP A 509 " ideal model delta sigma weight residual 116.34 110.19 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" C LEU A 144 " pdb=" N GLU A 145 " pdb=" CA GLU A 145 " ideal model delta sigma weight residual 121.80 131.64 -9.84 2.44e+00 1.68e-01 1.63e+01 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.14 114.18 -6.04 1.52e+00 4.33e-01 1.58e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 121.85 -7.45 2.30e+00 1.89e-01 1.05e+01 ... (remaining 9013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 3518 17.49 - 34.98: 355 34.98 - 52.46: 66 52.46 - 69.95: 16 69.95 - 87.44: 10 Dihedral angle restraints: 3965 sinusoidal: 1640 harmonic: 2325 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.96 -59.96 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 42.17 50.83 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 129.29 -36.29 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 3962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 609 0.037 - 0.073: 235 0.073 - 0.110: 73 0.110 - 0.147: 23 0.147 - 0.183: 3 Chirality restraints: 943 Sorted by residual: chirality pdb=" CA PRO B 521 " pdb=" N PRO B 521 " pdb=" C PRO B 521 " pdb=" CB PRO B 521 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" C3 NAG A 701 " pdb=" N2 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA CYS B 432 " pdb=" N CYS B 432 " pdb=" C CYS B 432 " pdb=" CB CYS B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 940 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO B 521 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 146 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 252 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.50e+00 pdb=" N PRO A 253 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.032 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 77 2.66 - 3.22: 6007 3.22 - 3.78: 9260 3.78 - 4.34: 12549 4.34 - 4.90: 21450 Nonbonded interactions: 49343 Sorted by model distance: nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 703 " model vdw 2.103 2.230 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.153 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.253 3.120 nonbonded pdb=" O PRO B 384 " pdb=" OG1 THR B 385 " model vdw 2.292 3.040 ... (remaining 49338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.880 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.200 Process input model: 24.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 0.078 6638 Z= 0.266 Angle : 0.636 9.844 9018 Z= 0.341 Chirality : 0.045 0.183 943 Planarity : 0.007 0.117 1169 Dihedral : 14.813 87.438 2452 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.46 % Favored : 94.03 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.30), residues: 787 helix: 0.61 (0.28), residues: 388 sheet: 0.04 (0.71), residues: 50 loop : -1.64 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 594 HIS 0.006 0.001 HIS A 378 PHE 0.023 0.001 PHE A 308 TYR 0.017 0.001 TYR A 381 ARG 0.006 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 0.771 Fit side-chains REVERT: A 78 LYS cc_start: 0.8354 (tptm) cc_final: 0.8014 (tptm) REVERT: A 216 ASN cc_start: 0.7667 (m-40) cc_final: 0.7430 (m-40) REVERT: A 402 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6352 (mm-30) REVERT: A 421 ILE cc_start: 0.8013 (tp) cc_final: 0.7812 (tp) REVERT: A 455 MET cc_start: 0.7398 (tmm) cc_final: 0.6952 (tmm) REVERT: A 479 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 508 ASN cc_start: 0.7589 (m-40) cc_final: 0.7296 (t0) REVERT: B 357 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7901 (ttp80) REVERT: B 438 SER cc_start: 0.7762 (t) cc_final: 0.7441 (t) REVERT: B 443 SER cc_start: 0.8240 (m) cc_final: 0.7986 (m) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.1987 time to fit residues: 55.1622 Evaluate side-chains 191 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 374 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6638 Z= 0.310 Angle : 0.635 10.257 9018 Z= 0.323 Chirality : 0.047 0.258 943 Planarity : 0.007 0.118 1169 Dihedral : 6.261 59.379 932 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.84 % Favored : 93.65 % Rotamer: Outliers : 1.75 % Allowed : 10.77 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.30), residues: 787 helix: 0.85 (0.27), residues: 391 sheet: -0.21 (0.67), residues: 53 loop : -1.53 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 PHE 0.013 0.001 PHE A 308 TYR 0.021 0.001 TYR A 385 ARG 0.004 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7616 (tp30) cc_final: 0.7341 (tp30) REVERT: A 78 LYS cc_start: 0.8365 (tptm) cc_final: 0.8044 (tptm) REVERT: A 87 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6565 (tm-30) REVERT: A 421 ILE cc_start: 0.8526 (tp) cc_final: 0.8277 (tp) REVERT: A 455 MET cc_start: 0.7448 (tmm) cc_final: 0.6982 (tmm) REVERT: A 470 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8059 (tttp) REVERT: A 479 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 508 ASN cc_start: 0.7721 (m-40) cc_final: 0.7352 (t0) REVERT: A 556 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7965 (mtpp) REVERT: B 438 SER cc_start: 0.7531 (t) cc_final: 0.7214 (t) REVERT: B 443 SER cc_start: 0.8293 (m) cc_final: 0.8038 (m) outliers start: 12 outliers final: 8 residues processed: 195 average time/residue: 0.1847 time to fit residues: 47.5645 Evaluate side-chains 197 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 24 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6638 Z= 0.218 Angle : 0.592 10.365 9018 Z= 0.298 Chirality : 0.043 0.271 943 Planarity : 0.006 0.118 1169 Dihedral : 5.850 59.511 929 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.83 % Favored : 94.66 % Rotamer: Outliers : 1.89 % Allowed : 13.97 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.30), residues: 787 helix: 0.91 (0.27), residues: 391 sheet: -0.17 (0.65), residues: 53 loop : -1.46 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.010 0.001 PHE A 308 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7602 (tp30) cc_final: 0.7355 (tp30) REVERT: A 78 LYS cc_start: 0.8365 (tptm) cc_final: 0.8045 (tptm) REVERT: A 87 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6485 (tm-30) REVERT: A 270 MET cc_start: 0.8890 (tpt) cc_final: 0.8162 (tpt) REVERT: A 350 ASP cc_start: 0.6946 (p0) cc_final: 0.6726 (p0) REVERT: A 421 ILE cc_start: 0.8457 (tp) cc_final: 0.8198 (tp) REVERT: A 455 MET cc_start: 0.7420 (tmm) cc_final: 0.6971 (tmm) REVERT: A 470 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7968 (tttp) REVERT: A 471 GLU cc_start: 0.6951 (pm20) cc_final: 0.6673 (pm20) REVERT: A 479 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 508 ASN cc_start: 0.7634 (m-40) cc_final: 0.7371 (t0) REVERT: A 556 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7955 (mtpp) REVERT: B 438 SER cc_start: 0.7569 (t) cc_final: 0.7240 (t) REVERT: B 443 SER cc_start: 0.8266 (m) cc_final: 0.8004 (m) outliers start: 13 outliers final: 6 residues processed: 188 average time/residue: 0.1866 time to fit residues: 46.0739 Evaluate side-chains 186 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 574 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 345 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6638 Z= 0.290 Angle : 0.613 10.294 9018 Z= 0.311 Chirality : 0.045 0.261 943 Planarity : 0.006 0.119 1169 Dihedral : 5.888 58.689 929 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.72 % Favored : 93.77 % Rotamer: Outliers : 2.33 % Allowed : 16.16 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.30), residues: 787 helix: 0.86 (0.27), residues: 392 sheet: -0.01 (0.65), residues: 53 loop : -1.53 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.006 0.001 HIS A 378 PHE 0.012 0.001 PHE A 308 TYR 0.019 0.001 TYR A 385 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7612 (tp30) cc_final: 0.7343 (tp30) REVERT: A 78 LYS cc_start: 0.8385 (tptm) cc_final: 0.8040 (tptm) REVERT: A 87 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6384 (tm-30) REVERT: A 270 MET cc_start: 0.8915 (tpt) cc_final: 0.8214 (tpt) REVERT: A 287 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7784 (mm-40) REVERT: A 350 ASP cc_start: 0.6939 (p0) cc_final: 0.6731 (p0) REVERT: A 402 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6481 (mm-30) REVERT: A 455 MET cc_start: 0.7458 (tmm) cc_final: 0.7019 (tmm) REVERT: A 470 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7976 (tttp) REVERT: A 479 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 508 ASN cc_start: 0.7666 (m-40) cc_final: 0.7374 (t0) REVERT: A 556 LYS cc_start: 0.8323 (ttmm) cc_final: 0.7971 (mtpp) REVERT: B 438 SER cc_start: 0.7582 (t) cc_final: 0.7200 (t) REVERT: B 443 SER cc_start: 0.8285 (m) cc_final: 0.8032 (m) outliers start: 16 outliers final: 12 residues processed: 199 average time/residue: 0.1698 time to fit residues: 45.1486 Evaluate side-chains 201 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 67 optimal weight: 0.0370 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 345 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6638 Z= 0.218 Angle : 0.604 10.373 9018 Z= 0.302 Chirality : 0.044 0.260 943 Planarity : 0.006 0.118 1169 Dihedral : 5.783 58.801 929 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.96 % Favored : 94.54 % Rotamer: Outliers : 2.18 % Allowed : 17.47 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.30), residues: 787 helix: 1.06 (0.27), residues: 385 sheet: -0.04 (0.65), residues: 53 loop : -1.53 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.010 0.001 PHE A 308 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7597 (tp30) cc_final: 0.7342 (tp30) REVERT: A 78 LYS cc_start: 0.8377 (tptm) cc_final: 0.8043 (tptm) REVERT: A 270 MET cc_start: 0.8912 (tpt) cc_final: 0.8220 (tpt) REVERT: A 287 GLN cc_start: 0.8054 (mm-40) cc_final: 0.7737 (mm-40) REVERT: A 350 ASP cc_start: 0.6966 (p0) cc_final: 0.6663 (p0) REVERT: A 455 MET cc_start: 0.7441 (tmm) cc_final: 0.6982 (tmm) REVERT: A 470 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7970 (tttp) REVERT: A 479 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 508 ASN cc_start: 0.7637 (m-40) cc_final: 0.7404 (t0) REVERT: A 556 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7962 (mtpp) REVERT: B 438 SER cc_start: 0.7533 (t) cc_final: 0.7240 (t) REVERT: B 443 SER cc_start: 0.8243 (m) cc_final: 0.7990 (m) outliers start: 15 outliers final: 11 residues processed: 187 average time/residue: 0.1730 time to fit residues: 43.3567 Evaluate side-chains 190 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 24 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6638 Z= 0.211 Angle : 0.593 10.332 9018 Z= 0.296 Chirality : 0.043 0.258 943 Planarity : 0.006 0.118 1169 Dihedral : 5.726 58.426 929 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.70 % Favored : 94.79 % Rotamer: Outliers : 2.62 % Allowed : 17.18 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.30), residues: 787 helix: 1.09 (0.27), residues: 385 sheet: -0.00 (0.66), residues: 53 loop : -1.49 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.010 0.001 PHE A 308 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7605 (tp30) cc_final: 0.7346 (tp30) REVERT: A 78 LYS cc_start: 0.8366 (tptm) cc_final: 0.8028 (tptm) REVERT: A 287 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7786 (mm-40) REVERT: A 350 ASP cc_start: 0.7000 (p0) cc_final: 0.6680 (p0) REVERT: A 455 MET cc_start: 0.7439 (tmm) cc_final: 0.6980 (tmm) REVERT: A 470 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7981 (tttp) REVERT: A 479 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 508 ASN cc_start: 0.7626 (m-40) cc_final: 0.7426 (t0) REVERT: A 556 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7963 (mtpp) REVERT: B 438 SER cc_start: 0.7573 (t) cc_final: 0.7261 (t) REVERT: B 443 SER cc_start: 0.8244 (m) cc_final: 0.7989 (m) outliers start: 18 outliers final: 17 residues processed: 182 average time/residue: 0.1692 time to fit residues: 41.5920 Evaluate side-chains 195 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 0.0020 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 601 ASN B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 6638 Z= 0.210 Angle : 0.595 10.295 9018 Z= 0.297 Chirality : 0.043 0.257 943 Planarity : 0.006 0.118 1169 Dihedral : 5.691 58.163 929 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.96 % Favored : 94.54 % Rotamer: Outliers : 2.91 % Allowed : 17.76 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.30), residues: 787 helix: 1.12 (0.27), residues: 385 sheet: -0.02 (0.67), residues: 53 loop : -1.47 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 378 PHE 0.011 0.001 PHE A 308 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7605 (tp30) cc_final: 0.7343 (tp30) REVERT: A 78 LYS cc_start: 0.8361 (tptm) cc_final: 0.8026 (tptm) REVERT: A 287 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7791 (mm-40) REVERT: A 350 ASP cc_start: 0.6978 (p0) cc_final: 0.6683 (p0) REVERT: A 455 MET cc_start: 0.7437 (tmm) cc_final: 0.6994 (tmm) REVERT: A 470 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7955 (tttp) REVERT: A 479 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 489 GLU cc_start: 0.7447 (pm20) cc_final: 0.7187 (pm20) REVERT: A 556 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7959 (mtpp) REVERT: B 438 SER cc_start: 0.7595 (t) cc_final: 0.7271 (t) REVERT: B 443 SER cc_start: 0.8236 (m) cc_final: 0.7982 (m) outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.1655 time to fit residues: 42.1600 Evaluate side-chains 194 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 271 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 470 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1166 > 50: distance: 27 - 170: 33.237 distance: 69 - 89: 30.604 distance: 85 - 89: 32.384 distance: 89 - 90: 20.481 distance: 90 - 91: 22.123 distance: 90 - 93: 26.979 distance: 91 - 92: 18.399 distance: 91 - 97: 48.917 distance: 93 - 94: 16.112 distance: 94 - 95: 9.472 distance: 94 - 96: 12.406 distance: 97 - 98: 5.229 distance: 98 - 99: 7.706 distance: 98 - 101: 21.904 distance: 99 - 100: 18.542 distance: 99 - 109: 35.316 distance: 101 - 102: 29.412 distance: 102 - 103: 15.476 distance: 102 - 104: 16.678 distance: 103 - 105: 20.949 distance: 104 - 106: 32.515 distance: 105 - 107: 31.374 distance: 106 - 107: 14.791 distance: 107 - 108: 26.752 distance: 109 - 110: 33.760 distance: 110 - 111: 34.659 distance: 110 - 113: 35.117 distance: 111 - 112: 40.317 distance: 111 - 118: 14.330 distance: 113 - 114: 25.674 distance: 114 - 115: 15.044 distance: 115 - 116: 39.098 distance: 116 - 117: 36.190 distance: 118 - 119: 15.502 distance: 119 - 120: 44.993 distance: 119 - 122: 46.472 distance: 120 - 121: 20.015 distance: 120 - 126: 48.227 distance: 122 - 123: 22.464 distance: 123 - 124: 44.040 distance: 123 - 125: 18.773 distance: 126 - 127: 14.195 distance: 126 - 132: 11.881 distance: 127 - 128: 36.157 distance: 127 - 130: 15.692 distance: 128 - 129: 4.312 distance: 128 - 133: 39.942 distance: 130 - 131: 42.262 distance: 131 - 132: 30.118 distance: 133 - 134: 23.924 distance: 134 - 135: 52.911 distance: 134 - 137: 28.196 distance: 135 - 136: 25.508 distance: 135 - 141: 43.287 distance: 137 - 138: 21.549 distance: 138 - 139: 29.414 distance: 138 - 140: 34.413 distance: 141 - 142: 29.261 distance: 142 - 143: 20.090 distance: 142 - 145: 6.991 distance: 143 - 149: 56.392 distance: 145 - 146: 35.242 distance: 146 - 147: 34.769 distance: 146 - 148: 27.017 distance: 149 - 150: 10.007 distance: 150 - 151: 36.520 distance: 150 - 153: 17.693 distance: 151 - 152: 13.390 distance: 151 - 160: 16.946 distance: 153 - 154: 27.796 distance: 154 - 155: 8.691 distance: 155 - 157: 15.618 distance: 156 - 158: 35.479 distance: 157 - 159: 25.399 distance: 158 - 159: 13.316 distance: 160 - 161: 10.059 distance: 161 - 162: 11.238 distance: 161 - 164: 26.549 distance: 162 - 163: 28.315 distance: 162 - 167: 39.319 distance: 164 - 165: 15.370 distance: 164 - 166: 33.024 distance: 167 - 168: 44.059 distance: 168 - 169: 20.517 distance: 169 - 170: 39.133 distance: 169 - 171: 22.464