Starting phenix.real_space_refine on Sun Mar 17 11:29:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2v_23142/03_2024/7l2v_23142_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2v_23142/03_2024/7l2v_23142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2v_23142/03_2024/7l2v_23142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2v_23142/03_2024/7l2v_23142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2v_23142/03_2024/7l2v_23142_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2v_23142/03_2024/7l2v_23142_updated.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 100 5.16 5 Na 1 4.78 5 C 11543 2.51 5 N 2813 2.21 5 O 3137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "D PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17594 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "D" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "B" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' NA': 1, '6EU': 1, 'XPS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.62, per 1000 atoms: 0.55 Number of scatterers: 17594 At special positions: 0 Unit cell: (126.92, 126.92, 111.055, 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) S 100 16.00 Na 1 11.00 O 3137 8.00 N 2813 7.00 C 11543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.91 Conformation dependent library (CDL) restraints added in 3.1 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 4 sheets defined 57.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 4.220A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 598 removed outlier: 4.320A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 656 through 671 Processing helix chain 'A' and resid 673 through 710 removed outlier: 3.620A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 4.269A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 598 removed outlier: 4.335A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 Processing helix chain 'D' and resid 656 through 671 Processing helix chain 'D' and resid 674 through 710 removed outlier: 3.661A pdb=" N ILE D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER D 693 " --> pdb=" O ILE D 689 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 4.310A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 598 removed outlier: 3.822A pdb=" N ARG B 575 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP B 576 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU B 577 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS B 578 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET B 581 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 591 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 593 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 596 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 673 through 689 removed outlier: 3.562A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 710 removed outlier: 4.208A pdb=" N LYS B 694 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP B 697 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.195A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 574 removed outlier: 3.561A pdb=" N ALA C 566 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 567 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 598 removed outlier: 4.544A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 656 through 671 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 691 through 710 removed outlier: 4.473A pdb=" N LYS C 694 " --> pdb=" O GLN C 691 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 696 " --> pdb=" O SER C 693 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 6.336A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 742 through 747 removed outlier: 6.279A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 6.225A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 6.140A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 874 hydrogen bonds defined for protein. 2190 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: 4.83 Time building geometry restraints manager: 7.46 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: 5074 1.34 - 1.46: 3623 1.46 - 1.58: 9171 1.58 - 1.70: 0 1.70 - 1.81: 164 Bond restraints: 18032 Sorted by residual: bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.450 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C GLU A 249 " pdb=" N LEU A 250 " ideal model delta sigma weight residual 1.331 1.372 -0.040 1.59e-02 3.96e+03 6.46e+00 ... (remaining 18027 not shown) Histogram of bond angle deviations from ideal: 95.75 - 103.41: 167 103.41 - 111.06: 6651 111.06 - 118.72: 7353 118.72 - 126.38: 10095 126.38 - 134.04: 197 Bond angle restraints: 24463 Sorted by residual: angle pdb=" C CYS A 390 " pdb=" N GLU A 391 " pdb=" CA GLU A 391 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" C CYS B 390 " pdb=" N GLU B 391 " pdb=" CA GLU B 391 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C CYS C 390 " pdb=" N GLU C 391 " pdb=" CA GLU C 391 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" CBM 6EU A 901 " pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 110.82 120.81 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N PHE B 712 " pdb=" CA PHE B 712 " pdb=" C PHE B 712 " ideal model delta sigma weight residual 110.80 117.87 -7.07 2.13e+00 2.20e-01 1.10e+01 ... (remaining 24458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 10145 16.06 - 32.12: 606 32.12 - 48.18: 88 48.18 - 64.24: 29 64.24 - 80.30: 17 Dihedral angle restraints: 10885 sinusoidal: 4565 harmonic: 6320 Sorted by residual: dihedral pdb=" CA VAL C 415 " pdb=" C VAL C 415 " pdb=" N GLU C 416 " pdb=" CA GLU C 416 " ideal model delta harmonic sigma weight residual -180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 10882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2640 0.090 - 0.180: 107 0.180 - 0.269: 1 0.269 - 0.359: 0 0.359 - 0.449: 4 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CAO 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAR 6EU D 901 " pdb=" CAW 6EU D 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.66 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 2749 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 541 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C MET A 541 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A 541 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 542 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 700 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C GLN D 700 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN D 700 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG D 701 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 539 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ALA B 539 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA B 539 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 540 " -0.016 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 180 2.63 - 3.19: 16403 3.19 - 3.76: 26657 3.76 - 4.33: 36772 4.33 - 4.90: 60778 Nonbonded interactions: 140790 Sorted by model distance: nonbonded pdb=" O1 XPS B 902 " pdb=" O4 XPS B 902 " model vdw 2.056 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.203 2.440 nonbonded pdb=" NH2 ARG A 557 " pdb=" OE1 GLU A 570 " model vdw 2.229 2.520 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.229 2.440 ... (remaining 140785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 193 through 751 or resid 901)) selection = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.050 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 46.670 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 18032 Z= 0.477 Angle : 0.850 9.985 24463 Z= 0.449 Chirality : 0.046 0.449 2752 Planarity : 0.005 0.034 3012 Dihedral : 11.254 80.300 6829 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.37 % Allowed : 0.79 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.76 (0.17), residues: 2136 helix: 1.58 (0.14), residues: 1260 sheet: -0.70 (0.46), residues: 84 loop : -1.13 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 372 HIS 0.006 0.001 HIS A 320 PHE 0.042 0.002 PHE C 304 TYR 0.017 0.002 TYR A 738 ARG 0.009 0.001 ARG C 721 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 729 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 TYR cc_start: 0.6752 (m-80) cc_final: 0.5854 (m-80) REVERT: A 378 HIS cc_start: 0.7887 (p-80) cc_final: 0.6588 (p-80) REVERT: A 504 LYS cc_start: 0.8996 (mttt) cc_final: 0.8522 (mmmt) REVERT: A 536 GLU cc_start: 0.8797 (mp0) cc_final: 0.8464 (mp0) REVERT: A 688 LYS cc_start: 0.9008 (tttt) cc_final: 0.8500 (tppt) REVERT: D 250 LEU cc_start: 0.8592 (mt) cc_final: 0.8389 (mp) REVERT: D 253 SER cc_start: 0.9468 (m) cc_final: 0.8819 (p) REVERT: D 326 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8562 (mt-10) REVERT: D 383 ASP cc_start: 0.7942 (p0) cc_final: 0.7514 (t0) REVERT: D 406 THR cc_start: 0.8436 (m) cc_final: 0.8123 (p) REVERT: D 410 HIS cc_start: 0.8264 (m-70) cc_final: 0.7569 (m-70) REVERT: D 506 LEU cc_start: 0.9414 (tp) cc_final: 0.9202 (tp) REVERT: D 510 SER cc_start: 0.9152 (m) cc_final: 0.8858 (p) REVERT: D 511 TYR cc_start: 0.9088 (t80) cc_final: 0.8716 (t80) REVERT: D 562 MET cc_start: 0.8760 (mmm) cc_final: 0.8257 (mmp) REVERT: D 688 LYS cc_start: 0.8890 (tptt) cc_final: 0.8651 (tptt) REVERT: D 697 TRP cc_start: 0.8430 (t60) cc_final: 0.7843 (t60) REVERT: D 738 TYR cc_start: 0.8102 (m-80) cc_final: 0.7841 (m-80) REVERT: B 222 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8533 (mm-30) REVERT: B 315 LEU cc_start: 0.9553 (mt) cc_final: 0.9339 (mp) REVERT: B 326 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8588 (mt-10) REVERT: B 368 LYS cc_start: 0.8024 (tttt) cc_final: 0.7512 (tttt) REVERT: B 378 HIS cc_start: 0.8192 (p-80) cc_final: 0.7955 (p-80) REVERT: B 397 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8297 (mt-10) REVERT: B 423 GLN cc_start: 0.8546 (tp40) cc_final: 0.8207 (tp-100) REVERT: B 656 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8594 (tptm) REVERT: C 202 GLN cc_start: 0.8073 (tt0) cc_final: 0.7704 (tm-30) REVERT: C 203 THR cc_start: 0.8140 (t) cc_final: 0.7539 (p) REVERT: C 228 GLN cc_start: 0.8432 (mt0) cc_final: 0.8087 (pm20) REVERT: C 308 MET cc_start: 0.9168 (mmm) cc_final: 0.8884 (mmm) REVERT: C 309 TYR cc_start: 0.9186 (t80) cc_final: 0.8941 (t80) REVERT: C 324 LYS cc_start: 0.8878 (mttt) cc_final: 0.8511 (mttm) REVERT: C 359 GLU cc_start: 0.8287 (tt0) cc_final: 0.7971 (tt0) REVERT: C 378 HIS cc_start: 0.8234 (p-80) cc_final: 0.6583 (p90) REVERT: C 397 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 406 THR cc_start: 0.8420 (m) cc_final: 0.8066 (p) REVERT: C 423 GLN cc_start: 0.8568 (tp40) cc_final: 0.8266 (tp-100) REVERT: C 481 SER cc_start: 0.9600 (m) cc_final: 0.9132 (p) REVERT: C 506 LEU cc_start: 0.9545 (tp) cc_final: 0.9291 (tp) REVERT: C 510 SER cc_start: 0.8705 (m) cc_final: 0.8250 (p) REVERT: C 511 TYR cc_start: 0.9062 (t80) cc_final: 0.8833 (t80) REVERT: C 562 MET cc_start: 0.8854 (mmm) cc_final: 0.8481 (mmp) REVERT: C 592 SER cc_start: 0.9321 (t) cc_final: 0.9084 (p) outliers start: 7 outliers final: 0 residues processed: 734 average time/residue: 0.3090 time to fit residues: 329.2586 Evaluate side-chains 488 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 487 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 656 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN D 494 GLN D 700 GLN B 202 GLN B 378 HIS C 223 ASN C 700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18032 Z= 0.194 Angle : 0.572 6.210 24463 Z= 0.305 Chirality : 0.038 0.202 2752 Planarity : 0.005 0.039 3012 Dihedral : 5.989 59.580 2761 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.32 % Allowed : 10.71 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.10 (0.18), residues: 2136 helix: 1.92 (0.14), residues: 1260 sheet: -0.67 (0.45), residues: 84 loop : -1.10 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 740 HIS 0.003 0.001 HIS A 289 PHE 0.027 0.002 PHE B 720 TYR 0.016 0.001 TYR D 511 ARG 0.007 0.001 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 546 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8195 (pp20) REVERT: A 308 MET cc_start: 0.9152 (mmm) cc_final: 0.8491 (mtp) REVERT: A 374 TYR cc_start: 0.6527 (m-80) cc_final: 0.5613 (m-80) REVERT: A 504 LYS cc_start: 0.8927 (mttt) cc_final: 0.8525 (mmmt) REVERT: A 648 GLU cc_start: 0.8437 (tt0) cc_final: 0.8046 (pp20) REVERT: D 253 SER cc_start: 0.9373 (m) cc_final: 0.8932 (p) REVERT: D 308 MET cc_start: 0.9336 (mmm) cc_final: 0.9098 (mmm) REVERT: D 332 LYS cc_start: 0.9472 (mmmm) cc_final: 0.9212 (mtmm) REVERT: D 383 ASP cc_start: 0.7900 (p0) cc_final: 0.7469 (t0) REVERT: D 406 THR cc_start: 0.8410 (m) cc_final: 0.8127 (p) REVERT: D 410 HIS cc_start: 0.8259 (m-70) cc_final: 0.7886 (m-70) REVERT: D 716 MET cc_start: 0.6184 (tmm) cc_final: 0.5818 (tpt) REVERT: B 202 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: B 228 GLN cc_start: 0.7992 (mp10) cc_final: 0.7760 (mp10) REVERT: B 293 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 315 LEU cc_start: 0.9506 (mt) cc_final: 0.9263 (mp) REVERT: B 378 HIS cc_start: 0.8232 (p90) cc_final: 0.7270 (p-80) REVERT: B 397 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 423 GLN cc_start: 0.8558 (tp40) cc_final: 0.8293 (tp-100) REVERT: B 656 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8266 (mttt) REVERT: B 700 GLN cc_start: 0.9142 (tp40) cc_final: 0.8843 (tp40) REVERT: C 211 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8401 (mmt90) REVERT: C 219 LEU cc_start: 0.9566 (tp) cc_final: 0.9254 (tp) REVERT: C 222 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8467 (mt-10) REVERT: C 228 GLN cc_start: 0.8412 (mt0) cc_final: 0.8153 (pm20) REVERT: C 309 TYR cc_start: 0.9165 (t80) cc_final: 0.8923 (t80) REVERT: C 378 HIS cc_start: 0.7659 (p-80) cc_final: 0.7373 (p90) REVERT: C 403 SER cc_start: 0.8480 (p) cc_final: 0.8074 (m) REVERT: C 423 GLN cc_start: 0.8551 (tp40) cc_final: 0.8307 (tp40) REVERT: C 481 SER cc_start: 0.9559 (m) cc_final: 0.9131 (p) REVERT: C 520 SER cc_start: 0.9488 (p) cc_final: 0.9188 (t) REVERT: C 589 PHE cc_start: 0.8452 (t80) cc_final: 0.8172 (t80) REVERT: C 700 GLN cc_start: 0.9162 (mm110) cc_final: 0.8763 (tp-100) REVERT: C 746 GLU cc_start: 0.7682 (pt0) cc_final: 0.7232 (pt0) outliers start: 44 outliers final: 22 residues processed: 562 average time/residue: 0.2752 time to fit residues: 232.4455 Evaluate side-chains 507 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 483 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 393 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 53 optimal weight: 30.0000 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18032 Z= 0.234 Angle : 0.565 10.429 24463 Z= 0.295 Chirality : 0.039 0.271 2752 Planarity : 0.004 0.050 3012 Dihedral : 5.492 59.015 2761 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.43 % Allowed : 13.66 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.05 (0.18), residues: 2136 helix: 1.86 (0.14), residues: 1260 sheet: -0.42 (0.48), residues: 84 loop : -1.13 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 740 HIS 0.004 0.001 HIS D 378 PHE 0.023 0.001 PHE C 304 TYR 0.017 0.001 TYR C 584 ARG 0.008 0.000 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 482 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7664 (t80) cc_final: 0.6693 (t80) REVERT: A 308 MET cc_start: 0.9235 (mmm) cc_final: 0.8582 (mtp) REVERT: A 372 TRP cc_start: 0.7848 (p-90) cc_final: 0.7625 (p-90) REVERT: A 374 TYR cc_start: 0.6639 (m-80) cc_final: 0.5273 (m-80) REVERT: A 504 LYS cc_start: 0.8955 (mttt) cc_final: 0.8522 (mmmt) REVERT: A 562 MET cc_start: 0.8833 (mmm) cc_final: 0.8225 (mmm) REVERT: A 648 GLU cc_start: 0.8429 (tt0) cc_final: 0.8086 (pp20) REVERT: D 253 SER cc_start: 0.9383 (m) cc_final: 0.9040 (p) REVERT: D 383 ASP cc_start: 0.7944 (p0) cc_final: 0.7473 (t0) REVERT: D 406 THR cc_start: 0.8401 (m) cc_final: 0.8135 (p) REVERT: D 410 HIS cc_start: 0.8215 (m-70) cc_final: 0.7576 (m-70) REVERT: D 716 MET cc_start: 0.6167 (tmm) cc_final: 0.5923 (tpt) REVERT: B 228 GLN cc_start: 0.7989 (mp10) cc_final: 0.7757 (mp10) REVERT: B 293 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 397 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 423 GLN cc_start: 0.8589 (tp40) cc_final: 0.8330 (tp-100) REVERT: B 491 ARG cc_start: 0.9060 (mmm-85) cc_final: 0.8676 (mmm160) REVERT: B 656 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8724 (tttm) REVERT: B 700 GLN cc_start: 0.9218 (tp40) cc_final: 0.8875 (tp40) REVERT: C 228 GLN cc_start: 0.8390 (mt0) cc_final: 0.8128 (pm20) REVERT: C 308 MET cc_start: 0.9331 (mmm) cc_final: 0.8938 (mtp) REVERT: C 309 TYR cc_start: 0.9177 (t80) cc_final: 0.8888 (t80) REVERT: C 397 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 423 GLN cc_start: 0.8569 (tp40) cc_final: 0.8362 (tp-100) REVERT: C 481 SER cc_start: 0.9577 (m) cc_final: 0.9173 (p) REVERT: C 520 SER cc_start: 0.9446 (p) cc_final: 0.9225 (t) outliers start: 65 outliers final: 41 residues processed: 514 average time/residue: 0.2773 time to fit residues: 216.7376 Evaluate side-chains 496 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 454 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN D 228 GLN C 700 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18032 Z= 0.157 Angle : 0.528 10.360 24463 Z= 0.276 Chirality : 0.037 0.143 2752 Planarity : 0.004 0.042 3012 Dihedral : 4.992 53.799 2761 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.58 % Allowed : 16.09 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.11 (0.19), residues: 2136 helix: 1.92 (0.15), residues: 1260 sheet: 0.21 (0.52), residues: 76 loop : -1.18 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 372 HIS 0.007 0.001 HIS D 378 PHE 0.021 0.001 PHE B 304 TYR 0.020 0.001 TYR A 666 ARG 0.006 0.000 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 493 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7616 (t80) cc_final: 0.6953 (t80) REVERT: A 308 MET cc_start: 0.9201 (mmm) cc_final: 0.8526 (mtp) REVERT: A 372 TRP cc_start: 0.7835 (p-90) cc_final: 0.7625 (p-90) REVERT: A 374 TYR cc_start: 0.6621 (m-80) cc_final: 0.5279 (m-80) REVERT: A 504 LYS cc_start: 0.8959 (mttt) cc_final: 0.8532 (mmmt) REVERT: A 562 MET cc_start: 0.8829 (mmm) cc_final: 0.8248 (mmm) REVERT: A 648 GLU cc_start: 0.8436 (tt0) cc_final: 0.8149 (pp20) REVERT: D 253 SER cc_start: 0.9400 (m) cc_final: 0.9041 (p) REVERT: D 266 PHE cc_start: 0.8648 (t80) cc_final: 0.8369 (t80) REVERT: D 308 MET cc_start: 0.9257 (mmm) cc_final: 0.9018 (mmm) REVERT: D 383 ASP cc_start: 0.8070 (p0) cc_final: 0.7458 (t0) REVERT: D 384 LEU cc_start: 0.8517 (mt) cc_final: 0.8264 (mp) REVERT: D 406 THR cc_start: 0.8481 (m) cc_final: 0.8116 (p) REVERT: D 410 HIS cc_start: 0.8166 (m-70) cc_final: 0.7601 (m-70) REVERT: D 581 MET cc_start: 0.6352 (tpp) cc_final: 0.5964 (tpp) REVERT: D 585 LEU cc_start: 0.9364 (mt) cc_final: 0.9141 (mt) REVERT: D 700 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8565 (tm-30) REVERT: B 228 GLN cc_start: 0.8012 (mp10) cc_final: 0.7741 (mp10) REVERT: B 397 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 423 GLN cc_start: 0.8589 (tp40) cc_final: 0.8381 (tp-100) REVERT: B 491 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8617 (mmm160) REVERT: B 656 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8662 (tttm) REVERT: B 663 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8997 (mm) REVERT: C 228 GLN cc_start: 0.8411 (mt0) cc_final: 0.8162 (pm20) REVERT: C 308 MET cc_start: 0.9314 (mmm) cc_final: 0.8916 (mtp) REVERT: C 309 TYR cc_start: 0.9159 (t80) cc_final: 0.8873 (t80) REVERT: C 323 LEU cc_start: 0.8191 (mp) cc_final: 0.7963 (tp) REVERT: C 481 SER cc_start: 0.9589 (m) cc_final: 0.9189 (p) REVERT: C 520 SER cc_start: 0.9413 (p) cc_final: 0.9178 (t) REVERT: C 700 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8925 (mm-40) outliers start: 49 outliers final: 31 residues processed: 522 average time/residue: 0.2677 time to fit residues: 213.8734 Evaluate side-chains 491 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 458 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 736 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18032 Z= 0.165 Angle : 0.529 10.826 24463 Z= 0.274 Chirality : 0.037 0.173 2752 Planarity : 0.004 0.049 3012 Dihedral : 4.805 50.794 2761 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.69 % Allowed : 16.88 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.12 (0.19), residues: 2136 helix: 1.97 (0.15), residues: 1240 sheet: 0.21 (0.53), residues: 76 loop : -1.18 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 372 HIS 0.007 0.001 HIS D 378 PHE 0.023 0.001 PHE A 266 TYR 0.015 0.001 TYR A 666 ARG 0.005 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 485 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7802 (t80) cc_final: 0.7344 (t80) REVERT: A 308 MET cc_start: 0.9286 (mmm) cc_final: 0.8934 (tpp) REVERT: A 374 TYR cc_start: 0.6574 (m-80) cc_final: 0.5201 (m-80) REVERT: A 481 SER cc_start: 0.9594 (m) cc_final: 0.9227 (p) REVERT: A 562 MET cc_start: 0.8880 (mmm) cc_final: 0.8609 (mmm) REVERT: A 601 ASP cc_start: 0.7549 (t0) cc_final: 0.7212 (p0) REVERT: A 648 GLU cc_start: 0.8473 (tt0) cc_final: 0.8145 (pp20) REVERT: D 253 SER cc_start: 0.9395 (m) cc_final: 0.9051 (p) REVERT: D 266 PHE cc_start: 0.8632 (t80) cc_final: 0.8402 (t80) REVERT: D 383 ASP cc_start: 0.8158 (p0) cc_final: 0.7533 (t0) REVERT: D 384 LEU cc_start: 0.8558 (mt) cc_final: 0.8224 (mt) REVERT: D 406 THR cc_start: 0.8422 (m) cc_final: 0.8090 (p) REVERT: D 410 HIS cc_start: 0.8211 (m-70) cc_final: 0.7504 (m-70) REVERT: D 581 MET cc_start: 0.6236 (tpp) cc_final: 0.5803 (tpp) REVERT: D 585 LEU cc_start: 0.9373 (mt) cc_final: 0.9050 (mt) REVERT: B 228 GLN cc_start: 0.8012 (mp10) cc_final: 0.7739 (mp10) REVERT: B 397 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 453 TYR cc_start: 0.8446 (t80) cc_final: 0.8044 (t80) REVERT: B 491 ARG cc_start: 0.9027 (mmm-85) cc_final: 0.8590 (mmm160) REVERT: B 656 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8606 (tttp) REVERT: B 700 GLN cc_start: 0.9221 (tp40) cc_final: 0.9013 (tp40) REVERT: C 228 GLN cc_start: 0.8393 (mt0) cc_final: 0.8160 (pm20) REVERT: C 308 MET cc_start: 0.9322 (mmm) cc_final: 0.8856 (mtp) REVERT: C 309 TYR cc_start: 0.9172 (t80) cc_final: 0.8910 (t80) REVERT: C 481 SER cc_start: 0.9601 (m) cc_final: 0.9210 (p) REVERT: C 700 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8912 (mm-40) outliers start: 70 outliers final: 45 residues processed: 516 average time/residue: 0.2663 time to fit residues: 210.7253 Evaluate side-chains 502 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 456 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 736 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN A 727 GLN B 228 GLN B 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18032 Z= 0.168 Angle : 0.537 10.717 24463 Z= 0.277 Chirality : 0.037 0.175 2752 Planarity : 0.004 0.043 3012 Dihedral : 4.660 47.390 2761 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.53 % Allowed : 18.30 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.08 (0.19), residues: 2136 helix: 1.93 (0.15), residues: 1240 sheet: 0.12 (0.55), residues: 76 loop : -1.16 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 372 HIS 0.008 0.001 HIS D 378 PHE 0.024 0.001 PHE A 266 TYR 0.017 0.001 TYR D 666 ARG 0.005 0.000 ARG D 717 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 472 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8008 (tt0) cc_final: 0.7741 (tp40) REVERT: A 304 PHE cc_start: 0.7687 (t80) cc_final: 0.7217 (t80) REVERT: A 308 MET cc_start: 0.9301 (mmm) cc_final: 0.8903 (tpp) REVERT: A 374 TYR cc_start: 0.6911 (m-80) cc_final: 0.6444 (m-80) REVERT: A 481 SER cc_start: 0.9605 (m) cc_final: 0.9227 (p) REVERT: A 562 MET cc_start: 0.8943 (mmm) cc_final: 0.8696 (mmm) REVERT: A 601 ASP cc_start: 0.7569 (t0) cc_final: 0.7221 (p0) REVERT: A 648 GLU cc_start: 0.8476 (tt0) cc_final: 0.8151 (pp20) REVERT: A 704 THR cc_start: 0.9171 (m) cc_final: 0.8910 (p) REVERT: D 253 SER cc_start: 0.9395 (m) cc_final: 0.9064 (p) REVERT: D 378 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.7048 (m90) REVERT: D 383 ASP cc_start: 0.8152 (p0) cc_final: 0.7474 (t0) REVERT: D 384 LEU cc_start: 0.8581 (mt) cc_final: 0.8242 (mt) REVERT: D 406 THR cc_start: 0.8450 (m) cc_final: 0.8089 (p) REVERT: D 410 HIS cc_start: 0.8257 (m-70) cc_final: 0.7519 (m-70) REVERT: D 412 MET cc_start: 0.8775 (mmm) cc_final: 0.8517 (mtt) REVERT: D 581 MET cc_start: 0.6333 (tpp) cc_final: 0.6049 (tpp) REVERT: B 386 CYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8120 (t) REVERT: B 397 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8116 (mt-10) REVERT: B 453 TYR cc_start: 0.8481 (t80) cc_final: 0.8224 (t80) REVERT: B 491 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8717 (mmm160) REVERT: B 656 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8530 (tttp) REVERT: B 663 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9095 (mm) REVERT: B 700 GLN cc_start: 0.9240 (tp40) cc_final: 0.9011 (tp40) REVERT: C 228 GLN cc_start: 0.8389 (mt0) cc_final: 0.8132 (pm20) REVERT: C 308 MET cc_start: 0.9334 (mmm) cc_final: 0.8847 (mtp) REVERT: C 309 TYR cc_start: 0.9175 (t80) cc_final: 0.8827 (t80) REVERT: C 700 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8885 (mm-40) outliers start: 67 outliers final: 47 residues processed: 504 average time/residue: 0.2647 time to fit residues: 206.4698 Evaluate side-chains 502 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 451 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 736 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 116 optimal weight: 0.0770 chunk 149 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18032 Z= 0.201 Angle : 0.552 11.174 24463 Z= 0.283 Chirality : 0.038 0.187 2752 Planarity : 0.004 0.044 3012 Dihedral : 4.647 46.047 2761 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.59 % Allowed : 18.46 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.03 (0.19), residues: 2136 helix: 1.88 (0.15), residues: 1244 sheet: -0.18 (0.54), residues: 76 loop : -1.15 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 372 HIS 0.009 0.001 HIS D 378 PHE 0.034 0.001 PHE D 266 TYR 0.016 0.001 TYR A 738 ARG 0.005 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 461 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7825 (t80) cc_final: 0.7423 (t80) REVERT: A 308 MET cc_start: 0.9316 (mmm) cc_final: 0.8926 (tpp) REVERT: A 481 SER cc_start: 0.9541 (m) cc_final: 0.9273 (p) REVERT: A 562 MET cc_start: 0.8982 (mmm) cc_final: 0.8734 (mmm) REVERT: A 601 ASP cc_start: 0.7604 (t0) cc_final: 0.7214 (p0) REVERT: A 648 GLU cc_start: 0.8474 (tt0) cc_final: 0.8136 (pp20) REVERT: A 704 THR cc_start: 0.9192 (m) cc_final: 0.8939 (p) REVERT: D 253 SER cc_start: 0.9390 (m) cc_final: 0.9057 (p) REVERT: D 383 ASP cc_start: 0.8118 (p0) cc_final: 0.7466 (t0) REVERT: D 384 LEU cc_start: 0.8632 (mt) cc_final: 0.8292 (mt) REVERT: D 406 THR cc_start: 0.8420 (m) cc_final: 0.8042 (p) REVERT: D 410 HIS cc_start: 0.8250 (m-70) cc_final: 0.7535 (m-70) REVERT: D 412 MET cc_start: 0.8816 (mmm) cc_final: 0.8555 (mtt) REVERT: D 581 MET cc_start: 0.6382 (tpp) cc_final: 0.6084 (tpp) REVERT: B 386 CYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8079 (t) REVERT: B 397 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 684 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8119 (tt0) REVERT: B 700 GLN cc_start: 0.9264 (tp40) cc_final: 0.9015 (tp40) REVERT: C 228 GLN cc_start: 0.8378 (mt0) cc_final: 0.8113 (pm20) REVERT: C 254 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8784 (mp) outliers start: 68 outliers final: 54 residues processed: 493 average time/residue: 0.2589 time to fit residues: 196.5415 Evaluate side-chains 505 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 449 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 736 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18032 Z= 0.190 Angle : 0.551 10.613 24463 Z= 0.283 Chirality : 0.038 0.189 2752 Planarity : 0.004 0.043 3012 Dihedral : 4.443 49.137 2757 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.48 % Allowed : 18.93 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.95 (0.19), residues: 2136 helix: 1.80 (0.15), residues: 1248 sheet: -0.20 (0.55), residues: 76 loop : -1.19 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 372 HIS 0.008 0.001 HIS D 378 PHE 0.023 0.001 PHE A 266 TYR 0.018 0.001 TYR B 309 ARG 0.006 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 470 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8291 (tp30) REVERT: A 304 PHE cc_start: 0.7660 (t80) cc_final: 0.7154 (t80) REVERT: A 308 MET cc_start: 0.9303 (mmm) cc_final: 0.8821 (tpp) REVERT: A 372 TRP cc_start: 0.7797 (p-90) cc_final: 0.7228 (p-90) REVERT: A 481 SER cc_start: 0.9620 (m) cc_final: 0.9247 (p) REVERT: A 562 MET cc_start: 0.9014 (mmm) cc_final: 0.8768 (mmm) REVERT: A 601 ASP cc_start: 0.7549 (t0) cc_final: 0.7199 (p0) REVERT: A 648 GLU cc_start: 0.8493 (tt0) cc_final: 0.8146 (pp20) REVERT: D 253 SER cc_start: 0.9402 (m) cc_final: 0.9057 (p) REVERT: D 383 ASP cc_start: 0.8139 (p0) cc_final: 0.7407 (t0) REVERT: D 384 LEU cc_start: 0.8630 (mt) cc_final: 0.8291 (mt) REVERT: D 406 THR cc_start: 0.8408 (m) cc_final: 0.8030 (p) REVERT: D 410 HIS cc_start: 0.8305 (m-70) cc_final: 0.7636 (m-70) REVERT: D 412 MET cc_start: 0.8818 (mmm) cc_final: 0.8573 (mtt) REVERT: D 696 ILE cc_start: 0.9552 (mt) cc_final: 0.9095 (mt) REVERT: D 716 MET cc_start: 0.6112 (ttm) cc_final: 0.5868 (tpt) REVERT: B 386 CYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8096 (t) REVERT: B 392 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8583 (mmtm) REVERT: B 393 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8172 (p0) REVERT: B 397 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8172 (mt-10) REVERT: B 491 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8649 (mmm160) REVERT: B 649 PHE cc_start: 0.5903 (m-80) cc_final: 0.5327 (m-10) REVERT: B 663 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8967 (mm) REVERT: B 700 GLN cc_start: 0.9271 (tp40) cc_final: 0.9007 (tp40) REVERT: C 228 GLN cc_start: 0.8338 (mt0) cc_final: 0.8103 (pm20) REVERT: C 254 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8742 (mp) REVERT: C 308 MET cc_start: 0.9323 (mmm) cc_final: 0.8989 (mtp) REVERT: C 700 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8893 (tp40) outliers start: 66 outliers final: 54 residues processed: 502 average time/residue: 0.2696 time to fit residues: 208.5676 Evaluate side-chains 508 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 450 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 736 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 190 optimal weight: 0.0270 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 189 optimal weight: 0.3980 chunk 125 optimal weight: 5.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 18032 Z= 0.151 Angle : 0.562 11.439 24463 Z= 0.285 Chirality : 0.038 0.212 2752 Planarity : 0.004 0.043 3012 Dihedral : 4.257 47.669 2757 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.43 % Allowed : 20.31 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.89 (0.19), residues: 2136 helix: 1.73 (0.15), residues: 1260 sheet: -0.08 (0.55), residues: 76 loop : -1.23 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 372 HIS 0.009 0.001 HIS D 378 PHE 0.026 0.001 PHE A 266 TYR 0.023 0.001 TYR B 309 ARG 0.006 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 475 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8220 (tp30) REVERT: A 304 PHE cc_start: 0.7860 (t80) cc_final: 0.7595 (t80) REVERT: A 308 MET cc_start: 0.9296 (mmm) cc_final: 0.8895 (tpp) REVERT: A 372 TRP cc_start: 0.7826 (p-90) cc_final: 0.7517 (p-90) REVERT: A 374 TYR cc_start: 0.6535 (m-10) cc_final: 0.5708 (m-80) REVERT: A 481 SER cc_start: 0.9529 (m) cc_final: 0.9268 (p) REVERT: A 562 MET cc_start: 0.9016 (mmm) cc_final: 0.8808 (mmm) REVERT: A 601 ASP cc_start: 0.7479 (t0) cc_final: 0.7187 (p0) REVERT: A 648 GLU cc_start: 0.8469 (tt0) cc_final: 0.8141 (pp20) REVERT: D 253 SER cc_start: 0.9401 (m) cc_final: 0.9045 (p) REVERT: D 383 ASP cc_start: 0.8193 (p0) cc_final: 0.7342 (t0) REVERT: D 384 LEU cc_start: 0.8617 (mt) cc_final: 0.8301 (mp) REVERT: D 406 THR cc_start: 0.8306 (m) cc_final: 0.7911 (p) REVERT: D 410 HIS cc_start: 0.8285 (m-70) cc_final: 0.7571 (m-70) REVERT: D 739 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8119 (mtm-85) REVERT: D 746 GLU cc_start: 0.6577 (pm20) cc_final: 0.6139 (pm20) REVERT: B 386 CYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8118 (t) REVERT: B 393 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8041 (p0) REVERT: B 397 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8102 (mt-10) REVERT: B 491 ARG cc_start: 0.8896 (mmm160) cc_final: 0.8641 (mmm160) REVERT: B 700 GLN cc_start: 0.9274 (tp40) cc_final: 0.9013 (tp40) REVERT: C 202 GLN cc_start: 0.7988 (tt0) cc_final: 0.7711 (tm-30) REVERT: C 228 GLN cc_start: 0.8375 (mt0) cc_final: 0.8151 (pm20) REVERT: C 254 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8734 (mp) REVERT: C 308 MET cc_start: 0.9326 (mmm) cc_final: 0.8971 (mtp) REVERT: C 700 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8872 (tp40) outliers start: 46 outliers final: 38 residues processed: 493 average time/residue: 0.2663 time to fit residues: 201.6430 Evaluate side-chains 503 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 462 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 589 PHE Chi-restraints excluded: chain B residue 736 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18032 Z= 0.213 Angle : 0.581 11.127 24463 Z= 0.296 Chirality : 0.039 0.212 2752 Planarity : 0.004 0.043 3012 Dihedral : 4.366 51.048 2757 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.64 % Allowed : 20.62 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.19), residues: 2136 helix: 1.71 (0.15), residues: 1260 sheet: -0.09 (0.55), residues: 76 loop : -1.26 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 372 HIS 0.008 0.001 HIS D 378 PHE 0.022 0.001 PHE A 266 TYR 0.023 0.001 TYR D 666 ARG 0.006 0.000 ARG A 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 464 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8235 (tp30) REVERT: A 304 PHE cc_start: 0.7868 (t80) cc_final: 0.7435 (t80) REVERT: A 308 MET cc_start: 0.9305 (mmm) cc_final: 0.8864 (tpp) REVERT: A 372 TRP cc_start: 0.7882 (p-90) cc_final: 0.7591 (p-90) REVERT: A 374 TYR cc_start: 0.6692 (m-10) cc_final: 0.5924 (m-80) REVERT: A 481 SER cc_start: 0.9616 (m) cc_final: 0.9278 (p) REVERT: A 562 MET cc_start: 0.9063 (mmm) cc_final: 0.8838 (mmm) REVERT: A 601 ASP cc_start: 0.7512 (t0) cc_final: 0.7204 (p0) REVERT: A 648 GLU cc_start: 0.8480 (tt0) cc_final: 0.8134 (pp20) REVERT: D 253 SER cc_start: 0.9396 (m) cc_final: 0.9039 (p) REVERT: D 383 ASP cc_start: 0.8135 (p0) cc_final: 0.7288 (t0) REVERT: D 384 LEU cc_start: 0.8625 (mt) cc_final: 0.8312 (mp) REVERT: D 406 THR cc_start: 0.8311 (m) cc_final: 0.7914 (p) REVERT: D 410 HIS cc_start: 0.8331 (m-70) cc_final: 0.7768 (m-70) REVERT: D 739 ARG cc_start: 0.8584 (mtp85) cc_final: 0.7979 (mtm-85) REVERT: D 746 GLU cc_start: 0.6600 (pm20) cc_final: 0.6162 (pm20) REVERT: B 214 MET cc_start: 0.8751 (pmm) cc_final: 0.8183 (pmm) REVERT: B 386 CYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8127 (t) REVERT: B 393 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8069 (p0) REVERT: B 397 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 700 GLN cc_start: 0.9261 (tp40) cc_final: 0.8975 (tp40) REVERT: B 716 MET cc_start: 0.5834 (tmm) cc_final: 0.5512 (tpp) REVERT: C 202 GLN cc_start: 0.8037 (tt0) cc_final: 0.7741 (tm-30) REVERT: C 228 GLN cc_start: 0.8320 (mt0) cc_final: 0.8101 (pm20) REVERT: C 254 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8808 (mp) REVERT: C 308 MET cc_start: 0.9343 (mmm) cc_final: 0.8976 (mtp) REVERT: C 397 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8185 (mt-10) outliers start: 50 outliers final: 43 residues processed: 484 average time/residue: 0.2591 time to fit residues: 193.5635 Evaluate side-chains 502 residues out of total 1896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 456 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 736 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 736 ASP Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 155 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 147 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 ASN B 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096271 restraints weight = 39074.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099239 restraints weight = 19179.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101231 restraints weight = 12535.042| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18032 Z= 0.152 Angle : 0.573 10.772 24463 Z= 0.289 Chirality : 0.038 0.216 2752 Planarity : 0.004 0.043 3012 Dihedral : 4.192 50.952 2757 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.43 % Allowed : 21.10 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.84 (0.19), residues: 2136 helix: 1.68 (0.15), residues: 1260 sheet: 0.07 (0.56), residues: 76 loop : -1.25 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 372 HIS 0.009 0.001 HIS D 378 PHE 0.026 0.001 PHE A 266 TYR 0.017 0.001 TYR A 554 ARG 0.006 0.000 ARG A 420 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4164.65 seconds wall clock time: 75 minutes 51.75 seconds (4551.75 seconds total)