Starting phenix.real_space_refine on Fri Mar 15 11:17:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iov_35626/03_2024/8iov_35626.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iov_35626/03_2024/8iov_35626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iov_35626/03_2024/8iov_35626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iov_35626/03_2024/8iov_35626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iov_35626/03_2024/8iov_35626.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iov_35626/03_2024/8iov_35626.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 4904 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4220 2.51 5 N 1075 2.21 5 O 1275 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 PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6607 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 4.06, per 1000 atoms: 0.61 Number of scatterers: 6607 At special positions: 0 Unit cell: (98.49, 72.36, 120.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1275 8.00 N 1075 7.00 C 4220 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=2.03 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 432 " " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " " NAG D 1 " - " ASN A 546 " " NAG E 1 " - " ASN A 90 " " NAG F 1 " - " ASN A 103 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 34 helices and 6 sheets defined 55.1% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.529A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.983A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.781A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix 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 220 through 252 removed outlier: 3.996A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 279 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.878A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.762A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.693A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.040A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.675A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.286A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.507A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.536A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.890A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.554A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.707A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.056A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.028A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.781A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.668A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 873 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: 1.73 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2080 1.34 - 1.46: 1702 1.46 - 1.58: 2951 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6791 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 MAN F 5 " pdb=" C2 MAN F 5 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 6786 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.53: 155 105.53 - 112.67: 3496 112.67 - 119.82: 2280 119.82 - 126.97: 3196 126.97 - 134.12: 105 Bond angle restraints: 9232 Sorted by residual: angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" C ASN A 432 " pdb=" CA ASN A 432 " pdb=" CB ASN A 432 " ideal model delta sigma weight residual 110.84 106.14 4.70 1.66e+00 3.63e-01 8.01e+00 angle pdb=" CB MET A 190 " pdb=" CG MET A 190 " pdb=" SD MET A 190 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.72e+00 angle pdb=" N GLU A 75 " pdb=" CA GLU A 75 " pdb=" CB GLU A 75 " ideal model delta sigma weight residual 110.16 114.01 -3.85 1.48e+00 4.57e-01 6.77e+00 angle pdb=" C ASP A 431 " pdb=" N ASN A 432 " pdb=" CA ASN A 432 " ideal model delta sigma weight residual 121.19 124.95 -3.76 1.59e+00 3.96e-01 5.59e+00 ... (remaining 9227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 3981 21.98 - 43.96: 180 43.96 - 65.94: 14 65.94 - 87.92: 17 87.92 - 109.90: 8 Dihedral angle restraints: 4200 sinusoidal: 1876 harmonic: 2324 Sorted by residual: 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 -86.00 -2.91 -83.09 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -132.94 46.94 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N GLU A 433 " pdb=" CA GLU A 433 " ideal model delta harmonic sigma weight residual 180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1006 0.230 - 0.459: 4 0.459 - 0.689: 1 0.689 - 0.919: 0 0.919 - 1.148: 1 Chirality restraints: 1012 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.25 -1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 1009 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 103 " -0.033 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" CG ASN A 103 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 103 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 103 " 0.041 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 432 " 0.017 2.00e-02 2.50e+03 1.67e-02 3.50e+00 pdb=" CG ASN A 432 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 432 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 432 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 610 " 0.011 2.00e-02 2.50e+03 1.09e-02 2.95e+00 pdb=" CG TRP A 610 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 610 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 610 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 610 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 610 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 610 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 610 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 610 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 610 " -0.000 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1075 2.76 - 3.29: 6290 3.29 - 3.83: 10695 3.83 - 4.36: 12048 4.36 - 4.90: 21060 Nonbonded interactions: 51168 Sorted by model distance: nonbonded pdb=" OG SER A 607 " pdb=" OD1 ASP A 609 " model vdw 2.222 2.440 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.242 2.440 nonbonded pdb=" O GLY A 268 " pdb=" ND2 ASN A 277 " model vdw 2.293 2.520 nonbonded pdb=" O ALA B 344 " pdb=" OG1 THR B 345 " model vdw 2.307 2.440 nonbonded pdb=" OE2 GLU A 489 " pdb=" OH TYR A 613 " model vdw 2.309 2.440 ... (remaining 51163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 11.920 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.570 Find NCS groups from input model: 0.170 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.003 0.038 6791 Z= 0.205 Angle : 0.621 9.756 9232 Z= 0.298 Chirality : 0.060 1.148 1012 Planarity : 0.003 0.041 1173 Dihedral : 13.944 109.902 2687 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 787 helix: 1.92 (0.26), residues: 397 sheet: 2.72 (0.76), residues: 42 loop : -0.63 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.007 0.001 PHE A 32 TYR 0.014 0.001 TYR A 50 ARG 0.001 0.000 ARG A 169 *********************** 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 57 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1680 time to fit residues: 13.6084 Evaluate side-chains 43 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 70 optimal weight: 0.0170 overall best weight: 0.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6791 Z= 0.129 Angle : 0.538 10.351 9232 Z= 0.262 Chirality : 0.045 0.364 1012 Planarity : 0.003 0.038 1173 Dihedral : 9.534 64.027 1165 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.58 % Allowed : 4.61 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.30), residues: 787 helix: 2.07 (0.26), residues: 394 sheet: 2.16 (0.73), residues: 42 loop : -0.63 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 401 PHE 0.008 0.001 PHE A 285 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG B 403 *********************** 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 52 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1808 time to fit residues: 12.7549 Evaluate side-chains 46 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 70 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6791 Z= 0.126 Angle : 0.508 10.799 9232 Z= 0.248 Chirality : 0.044 0.342 1012 Planarity : 0.003 0.036 1173 Dihedral : 7.269 53.597 1165 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.43 % Allowed : 6.34 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.30), residues: 787 helix: 2.17 (0.26), residues: 391 sheet: 1.94 (0.73), residues: 42 loop : -0.58 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.007 0.001 PHE A 523 TYR 0.010 0.001 TYR A 50 ARG 0.001 0.000 ARG A 169 *********************** 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 52 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.1668 time to fit residues: 12.3366 Evaluate side-chains 48 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.0470 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 20 optimal weight: 0.1980 chunk 62 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6791 Z= 0.121 Angle : 0.492 10.750 9232 Z= 0.241 Chirality : 0.043 0.335 1012 Planarity : 0.003 0.038 1173 Dihedral : 5.897 45.188 1165 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.72 % Allowed : 6.92 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 787 helix: 2.22 (0.26), residues: 392 sheet: 1.92 (0.72), residues: 42 loop : -0.52 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.007 0.001 PHE A 523 TYR 0.011 0.001 TYR A 50 ARG 0.001 0.000 ARG A 169 *********************** 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 54 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 471 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8470 (mp0) outliers start: 5 outliers final: 2 residues processed: 51 average time/residue: 0.1749 time to fit residues: 12.8382 Evaluate side-chains 49 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain B residue 392 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6791 Z= 0.219 Angle : 0.543 10.127 9232 Z= 0.271 Chirality : 0.043 0.343 1012 Planarity : 0.003 0.035 1173 Dihedral : 5.241 33.830 1165 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.43 % Allowed : 7.49 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.31), residues: 787 helix: 2.13 (0.26), residues: 396 sheet: 2.00 (0.77), residues: 41 loop : -0.50 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 610 HIS 0.005 0.001 HIS A 401 PHE 0.014 0.001 PHE B 347 TYR 0.013 0.001 TYR A 50 ARG 0.001 0.000 ARG B 498 *********************** 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 48 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8251 (mt-10) REVERT: B 471 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8402 (mp0) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.1730 time to fit residues: 11.1543 Evaluate side-chains 47 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6791 Z= 0.168 Angle : 0.515 10.248 9232 Z= 0.256 Chirality : 0.043 0.347 1012 Planarity : 0.003 0.037 1173 Dihedral : 4.868 33.539 1165 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.43 % Allowed : 8.50 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.31), residues: 787 helix: 2.14 (0.26), residues: 400 sheet: 2.00 (0.77), residues: 41 loop : -0.49 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.010 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.002 0.000 ARG A 169 *********************** 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 51 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8274 (mt-10) REVERT: B 471 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8333 (mp0) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.1930 time to fit residues: 13.1001 Evaluate side-chains 48 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6791 Z= 0.195 Angle : 0.525 9.937 9232 Z= 0.261 Chirality : 0.043 0.344 1012 Planarity : 0.003 0.037 1173 Dihedral : 4.707 33.387 1165 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.43 % Allowed : 8.50 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.31), residues: 787 helix: 2.13 (0.26), residues: 402 sheet: 1.95 (0.78), residues: 41 loop : -0.48 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.010 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG B 498 *********************** 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 49 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8443 (mp0) outliers start: 3 outliers final: 3 residues processed: 46 average time/residue: 0.1855 time to fit residues: 12.2779 Evaluate side-chains 48 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain B residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.0010 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6791 Z= 0.139 Angle : 0.519 10.910 9232 Z= 0.254 Chirality : 0.042 0.347 1012 Planarity : 0.003 0.039 1173 Dihedral : 4.489 32.694 1165 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.58 % Allowed : 8.79 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.31), residues: 787 helix: 2.16 (0.26), residues: 400 sheet: 2.01 (0.77), residues: 41 loop : -0.46 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.008 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 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 51 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.9363 (pttm) cc_final: 0.9162 (pttm) REVERT: A 267 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9017 (mm) REVERT: A 474 MET cc_start: 0.8858 (mmp) cc_final: 0.8604 (mmt) REVERT: B 471 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8499 (mp0) outliers start: 4 outliers final: 1 residues processed: 49 average time/residue: 0.1734 time to fit residues: 12.2252 Evaluate side-chains 47 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.0170 chunk 66 optimal weight: 0.0050 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6791 Z= 0.134 Angle : 0.509 11.122 9232 Z= 0.248 Chirality : 0.042 0.332 1012 Planarity : 0.003 0.039 1173 Dihedral : 4.269 32.196 1165 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.29 % Allowed : 9.22 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 787 helix: 2.24 (0.26), residues: 394 sheet: 2.03 (0.76), residues: 41 loop : -0.44 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.007 0.001 PHE A 523 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 9 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 48 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8950 (mm) REVERT: B 471 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8455 (mp0) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1770 time to fit residues: 11.8424 Evaluate side-chains 46 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6791 Z= 0.199 Angle : 0.551 10.703 9232 Z= 0.272 Chirality : 0.043 0.343 1012 Planarity : 0.003 0.038 1173 Dihedral : 4.310 31.493 1165 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.14 % Allowed : 9.94 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.31), residues: 787 helix: 2.18 (0.26), residues: 394 sheet: 1.95 (0.78), residues: 41 loop : -0.46 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 610 HIS 0.004 0.001 HIS A 401 PHE 0.010 0.001 PHE B 347 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG B 498 ********************** REFINEMENT MACRO_CYCLE 10 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 47 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 471 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8448 (mp0) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.1954 time to fit residues: 13.0533 Evaluate side-chains 47 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.0070 chunk 11 optimal weight: 0.1980 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.078769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.056366 restraints weight = 20793.877| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.18 r_work: 0.2814 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6791 Z= 0.135 Angle : 0.521 11.287 9232 Z= 0.254 Chirality : 0.042 0.342 1012 Planarity : 0.003 0.040 1173 Dihedral : 4.162 31.380 1165 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.29 % Allowed : 9.51 % Favored : 90.20 % 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: 1.57 (0.31), residues: 787 helix: 2.20 (0.26), residues: 394 sheet: 1.95 (0.76), residues: 41 loop : -0.42 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 610 HIS 0.003 0.001 HIS A 401 PHE 0.007 0.001 PHE B 342 TYR 0.012 0.001 TYR A 50 ARG 0.001 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.60 seconds wall clock time: 31 minutes 26.86 seconds (1886.86 seconds total)