Starting phenix.real_space_refine on Fri Feb 16 17:21:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/02_2024/7l2m_23133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/02_2024/7l2m_23133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/02_2024/7l2m_23133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/02_2024/7l2m_23133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/02_2024/7l2m_23133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/02_2024/7l2m_23133_updated.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 118 5.16 5 Na 3 4.78 5 C 10504 2.51 5 N 2530 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 428": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15981 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3653 Classifications: {'peptide': 446} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 434} Chain breaks: 1 Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {' NA': 1, '6EU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.97, per 1000 atoms: 0.56 Number of scatterers: 15981 At special positions: 0 Unit cell: (131.1, 132.24, 114, 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 118 16.00 Na 3 11.00 O 2826 8.00 N 2530 7.00 C 10504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.04 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.04 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.04 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.38 Conformation dependent library (CDL) restraints added in 2.9 seconds 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 6 sheets defined 54.8% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.691A pdb=" N TYR A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) 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 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.340A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 414' Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 removed outlier: 3.776A pdb=" N PHE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 511 through 532 Processing helix chain 'A' and resid 536 through 556 removed outlier: 4.382A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 removed outlier: 4.218A pdb=" N ILE A 569 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 5.174A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.731A pdb=" N ILE A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 689 removed outlier: 3.608A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 711 removed outlier: 4.072A pdb=" N TRP A 697 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 703 " --> pdb=" O GLN A 700 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A 707 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU A 709 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 710 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.752A pdb=" N TYR C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 399 No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 409 through 414 removed outlier: 4.347A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 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 532 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.047A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 575 removed outlier: 4.084A pdb=" N ILE C 569 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 598 removed outlier: 5.151A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.326A 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 670 removed outlier: 3.731A pdb=" N ILE C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 removed outlier: 3.603A pdb=" N ILE C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 711 removed outlier: 3.645A pdb=" N THR C 704 " --> pdb=" O GLN C 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.755A pdb=" N TYR D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 399 No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.149A pdb=" N LEU D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 409 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 532 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.998A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 575 removed outlier: 4.036A pdb=" N ILE D 569 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 598 removed outlier: 5.171A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 Processing helix chain 'D' and resid 656 through 670 removed outlier: 3.719A pdb=" N ILE D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 688 Processing helix chain 'D' and resid 692 through 711 removed outlier: 4.267A pdb=" N ILE D 703 " --> pdb=" O GLN D 700 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 707 " --> pdb=" O THR D 704 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D 709 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 710 " --> pdb=" O ASP D 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.768A pdb=" N TYR B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 399 No H-bonds generated for 'chain 'B' and resid 396 through 399' Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.252A pdb=" N LEU B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 409 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 532 Processing helix chain 'B' and resid 536 through 556 removed outlier: 4.379A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 removed outlier: 4.139A pdb=" N ILE B 569 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 removed outlier: 5.165A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.698A pdb=" N ILE B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 689 removed outlier: 3.673A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 711 removed outlier: 3.694A pdb=" N THR B 704 " --> pdb=" O GLN B 700 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 4.167A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 742 through 747 removed outlier: 4.227A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 742 through 747 removed outlier: 4.127A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 742 through 747 removed outlier: 4.228A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 61 through 63 Processing sheet with id= F, first strand: chain 'F' and resid 61 through 63 761 hydrogen bonds defined for protein. 2004 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: 4.00 Time building geometry restraints manager: 6.85 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: 4750 1.34 - 1.46: 3920 1.46 - 1.58: 7542 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 16392 Sorted by residual: bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" CAL 6EU A 901 " pdb=" CAM 6EU A 901 " ideal model delta sigma weight residual 1.560 1.517 0.043 2.00e-02 2.50e+03 4.59e+00 ... (remaining 16387 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.87: 376 106.87 - 113.65: 8949 113.65 - 120.43: 6955 120.43 - 127.22: 5798 127.22 - 134.00: 146 Bond angle restraints: 22224 Sorted by residual: angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.18e+01 angle pdb=" C SER B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" CBM 6EU D 901 " pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 110.82 120.39 -9.57 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CBM 6EU B 901 " pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 110.82 120.38 -9.56 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CBM 6EU A 901 " pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 110.82 120.38 -9.56 3.00e+00 1.11e-01 1.01e+01 ... (remaining 22219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 9284 17.84 - 35.67: 524 35.67 - 53.51: 101 53.51 - 71.34: 21 71.34 - 89.18: 18 Dihedral angle restraints: 9948 sinusoidal: 4238 harmonic: 5710 Sorted by residual: dihedral pdb=" CA PHE B 712 " pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA SER D 722 " pdb=" C SER D 722 " pdb=" N GLY D 723 " pdb=" CA GLY D 723 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 9945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1873 0.048 - 0.096: 531 0.096 - 0.145: 63 0.145 - 0.193: 1 0.193 - 0.241: 4 Chirality restraints: 2472 Sorted by residual: chirality pdb=" CAO 6EU C 901 " pdb=" CAJ 6EU C 901 " pdb=" CAR 6EU C 901 " pdb=" CAW 6EU C 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.48 0.24 2.00e-01 2.50e+01 1.45e+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 -2.48 0.24 2.00e-01 2.50e+01 1.45e+00 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 -2.48 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2469 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 444 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C TYR A 444 " 0.040 2.00e-02 2.50e+03 pdb=" O TYR A 444 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 445 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 438 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C PHE A 438 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE A 438 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 439 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 442 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.77e+00 pdb=" C CYS A 442 " -0.038 2.00e-02 2.50e+03 pdb=" O CYS A 442 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 443 " 0.013 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1684 2.74 - 3.28: 16218 3.28 - 3.82: 23903 3.82 - 4.36: 27885 4.36 - 4.90: 47607 Nonbonded interactions: 117297 Sorted by model distance: nonbonded pdb=" OH TYR D 584 " pdb=" OG1 THR D 641 " model vdw 2.196 2.440 nonbonded pdb=" N GLU C 536 " pdb=" OE1 GLU C 536 " model vdw 2.264 2.520 nonbonded pdb=" N GLU D 536 " pdb=" OE1 GLU D 536 " model vdw 2.267 2.520 nonbonded pdb=" OH TYR C 584 " pdb=" OG1 THR C 641 " model vdw 2.270 2.440 nonbonded pdb=" N GLU A 536 " pdb=" OE1 GLU A 536 " model vdw 2.279 2.520 ... (remaining 117292 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' and (resid 280 through 749 or resid 901)) selection = (chain 'B' and (resid 280 through 749 or resid 901)) selection = (chain 'C' and (resid 280 through 749 or resid 901)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.610 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: 3.380 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.630 Find NCS groups from input model: 1.060 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 16392 Z= 0.441 Angle : 0.778 9.573 22224 Z= 0.412 Chirality : 0.042 0.241 2472 Planarity : 0.004 0.052 2724 Dihedral : 12.367 89.181 6244 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.75 % Allowed : 4.08 % Favored : 95.17 % 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: 0.06 (0.19), residues: 1914 helix: 1.51 (0.15), residues: 1028 sheet: 0.19 (0.67), residues: 64 loop : -1.98 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 549 HIS 0.004 0.001 HIS D 364 PHE 0.015 0.002 PHE B 304 TYR 0.014 0.002 TYR A 444 ARG 0.003 0.001 ARG C 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 541 time to evaluate : 2.340 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: A 300 ASP cc_start: 0.8199 (m-30) cc_final: 0.7603 (p0) REVERT: A 403 SER cc_start: 0.8282 (p) cc_final: 0.8070 (t) REVERT: A 411 ASP cc_start: 0.7860 (m-30) cc_final: 0.7646 (m-30) REVERT: A 423 GLN cc_start: 0.9048 (tp40) cc_final: 0.8744 (tp-100) REVERT: A 536 GLU cc_start: 0.8830 (mp0) cc_final: 0.8612 (mp0) REVERT: A 551 ASN cc_start: 0.9235 (p0) cc_final: 0.8986 (p0) REVERT: A 576 ASP cc_start: 0.8838 (t0) cc_final: 0.8110 (m-30) REVERT: A 639 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8949 (ttmt) REVERT: A 653 TYR cc_start: 0.8476 (m-10) cc_final: 0.8218 (m-80) REVERT: A 697 TRP cc_start: 0.8712 (t60) cc_final: 0.7839 (t60) REVERT: C 300 ASP cc_start: 0.8174 (m-30) cc_final: 0.7547 (p0) REVERT: C 416 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: C 510 SER cc_start: 0.8933 (m) cc_final: 0.8694 (p) REVERT: C 551 ASN cc_start: 0.9314 (p0) cc_final: 0.9019 (p0) REVERT: C 561 GLN cc_start: 0.8342 (mp10) cc_final: 0.8139 (mp10) REVERT: C 564 ILE cc_start: 0.8941 (tt) cc_final: 0.8592 (mm) REVERT: C 576 ASP cc_start: 0.8836 (t0) cc_final: 0.7845 (m-30) REVERT: C 579 ARG cc_start: 0.6954 (mmt180) cc_final: 0.6522 (mtm-85) REVERT: C 580 PHE cc_start: 0.8835 (t80) cc_final: 0.8600 (t80) REVERT: C 639 LYS cc_start: 0.9339 (mtmt) cc_final: 0.8885 (mttt) REVERT: C 666 TYR cc_start: 0.9551 (t80) cc_final: 0.9335 (t80) REVERT: C 696 ILE cc_start: 0.8867 (mt) cc_final: 0.8603 (mt) REVERT: D 296 ASP cc_start: 0.6407 (p0) cc_final: 0.5900 (p0) REVERT: D 300 ASP cc_start: 0.8082 (m-30) cc_final: 0.7722 (p0) REVERT: D 411 ASP cc_start: 0.8084 (m-30) cc_final: 0.7877 (m-30) REVERT: D 561 GLN cc_start: 0.8436 (mp10) cc_final: 0.8118 (mp10) REVERT: D 576 ASP cc_start: 0.8920 (t0) cc_final: 0.8193 (m-30) REVERT: D 653 TYR cc_start: 0.8586 (m-10) cc_final: 0.8341 (m-80) REVERT: D 666 TYR cc_start: 0.9490 (t80) cc_final: 0.9275 (t80) REVERT: B 560 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7587 (mm-40) REVERT: B 564 ILE cc_start: 0.9042 (tp) cc_final: 0.8807 (mm) REVERT: B 576 ASP cc_start: 0.8891 (t0) cc_final: 0.7988 (m-30) REVERT: B 628 ASN cc_start: 0.8085 (m110) cc_final: 0.7885 (m-40) REVERT: B 636 GLU cc_start: 0.8836 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 653 TYR cc_start: 0.8544 (m-10) cc_final: 0.8298 (m-80) REVERT: B 697 TRP cc_start: 0.8808 (t60) cc_final: 0.8397 (t60) REVERT: E 21 PHE cc_start: 0.7167 (m-80) cc_final: 0.6825 (m-10) REVERT: E 34 TYR cc_start: 0.7032 (m-80) cc_final: 0.6569 (m-80) REVERT: E 68 ILE cc_start: 0.9495 (mt) cc_final: 0.9240 (pt) REVERT: F 61 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.5895 (pt) REVERT: F 68 ILE cc_start: 0.9427 (mt) cc_final: 0.9175 (pt) outliers start: 13 outliers final: 6 residues processed: 548 average time/residue: 0.2792 time to fit residues: 223.5945 Evaluate side-chains 362 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 354 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9990 chunk 144 optimal weight: 0.0060 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 494 GLN C 289 HIS C 301 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN D 551 ASN D 560 GLN B 551 ASN B 676 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16392 Z= 0.146 Angle : 0.530 8.845 22224 Z= 0.275 Chirality : 0.038 0.159 2472 Planarity : 0.003 0.052 2724 Dihedral : 7.402 58.961 2522 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.49 % Favored : 94.41 % Rotamer: Outliers : 1.49 % Allowed : 12.47 % Favored : 86.03 % 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: 0.74 (0.20), residues: 1914 helix: 2.06 (0.16), residues: 1036 sheet: 0.53 (0.68), residues: 64 loop : -1.70 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 740 HIS 0.007 0.001 HIS B 289 PHE 0.016 0.001 PHE B 712 TYR 0.012 0.001 TYR D 666 ARG 0.004 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 438 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.7721 (m-30) cc_final: 0.7483 (m-30) REVERT: A 423 GLN cc_start: 0.9126 (tp40) cc_final: 0.8721 (tp-100) REVERT: A 551 ASN cc_start: 0.8973 (p0) cc_final: 0.8628 (p0) REVERT: A 560 GLN cc_start: 0.8042 (tp40) cc_final: 0.7449 (mm110) REVERT: C 300 ASP cc_start: 0.7887 (m-30) cc_final: 0.7572 (p0) REVERT: C 423 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8727 (tm-30) REVERT: C 579 ARG cc_start: 0.6476 (mmt180) cc_final: 0.5821 (mtt-85) REVERT: C 600 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7153 (mp0) REVERT: D 433 ILE cc_start: 0.9356 (tp) cc_final: 0.9113 (tt) REVERT: D 561 GLN cc_start: 0.8343 (mp10) cc_final: 0.8024 (mp10) REVERT: D 562 MET cc_start: 0.7918 (mtt) cc_final: 0.7590 (mtt) REVERT: B 628 ASN cc_start: 0.8117 (m110) cc_final: 0.7864 (m-40) REVERT: B 636 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8240 (mm-30) REVERT: E 68 ILE cc_start: 0.9422 (mt) cc_final: 0.9066 (pt) REVERT: F 14 LYS cc_start: 0.8113 (ptmt) cc_final: 0.7752 (ptpp) REVERT: F 34 TYR cc_start: 0.7494 (m-80) cc_final: 0.7273 (m-10) REVERT: F 47 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8664 (mm-30) REVERT: F 68 ILE cc_start: 0.9434 (mt) cc_final: 0.9048 (pt) outliers start: 26 outliers final: 15 residues processed: 447 average time/residue: 0.2708 time to fit residues: 182.6105 Evaluate side-chains 385 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 370 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain E residue 15 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 153 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN C 408 ASN C 410 HIS D 408 ASN D 419 ASN D 494 GLN B 410 HIS B 494 GLN B 676 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16392 Z= 0.303 Angle : 0.601 6.951 22224 Z= 0.314 Chirality : 0.040 0.135 2472 Planarity : 0.004 0.051 2724 Dihedral : 6.508 48.641 2511 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.48 % Allowed : 13.68 % Favored : 81.84 % 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: 0.33 (0.19), residues: 1914 helix: 1.77 (0.16), residues: 1008 sheet: 0.58 (0.71), residues: 64 loop : -1.85 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 740 HIS 0.007 0.001 HIS B 289 PHE 0.026 0.002 PHE C 580 TYR 0.016 0.001 TYR D 511 ARG 0.004 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 373 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9204 (tp40) cc_final: 0.8792 (tp-100) REVERT: A 503 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8831 (tt) REVERT: A 576 ASP cc_start: 0.8950 (t0) cc_final: 0.8104 (m-30) REVERT: A 636 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8533 (tp30) REVERT: C 300 ASP cc_start: 0.7837 (m-30) cc_final: 0.7526 (p0) REVERT: C 423 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8809 (tm-30) REVERT: C 503 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8799 (tt) REVERT: C 576 ASP cc_start: 0.8936 (t0) cc_final: 0.7867 (m-30) REVERT: C 630 LEU cc_start: 0.8984 (tp) cc_final: 0.8686 (tp) REVERT: D 503 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8743 (tt) REVERT: D 561 GLN cc_start: 0.8370 (mp10) cc_final: 0.8046 (mp10) REVERT: D 576 ASP cc_start: 0.9032 (t0) cc_final: 0.8164 (m-30) REVERT: D 636 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8457 (tp30) REVERT: B 503 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8757 (tt) REVERT: B 576 ASP cc_start: 0.9005 (t0) cc_final: 0.8192 (m-30) REVERT: B 628 ASN cc_start: 0.8166 (m110) cc_final: 0.7960 (m-40) REVERT: E 47 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8439 (mm-30) REVERT: E 68 ILE cc_start: 0.9468 (mt) cc_final: 0.9128 (pt) REVERT: F 21 PHE cc_start: 0.7178 (m-10) cc_final: 0.6936 (m-10) REVERT: F 34 TYR cc_start: 0.7361 (m-80) cc_final: 0.7084 (m-10) REVERT: F 47 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8597 (mm-30) REVERT: F 68 ILE cc_start: 0.9401 (mt) cc_final: 0.9080 (pt) outliers start: 78 outliers final: 53 residues processed: 391 average time/residue: 0.2617 time to fit residues: 154.6073 Evaluate side-chains 393 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 336 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 707 ASP Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.8980 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 0.0370 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN B 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16392 Z= 0.169 Angle : 0.519 7.425 22224 Z= 0.273 Chirality : 0.038 0.146 2472 Planarity : 0.003 0.050 2724 Dihedral : 5.730 46.078 2511 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.68 % Allowed : 15.52 % Favored : 80.80 % 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: 0.69 (0.20), residues: 1914 helix: 2.19 (0.17), residues: 992 sheet: 0.82 (0.73), residues: 64 loop : -1.79 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 740 HIS 0.008 0.001 HIS B 289 PHE 0.028 0.001 PHE C 580 TYR 0.012 0.001 TYR C 653 ARG 0.003 0.000 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 374 time to evaluate : 1.900 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: A 411 ASP cc_start: 0.7852 (m-30) cc_final: 0.7599 (m-30) REVERT: A 423 GLN cc_start: 0.9279 (tp40) cc_final: 0.8907 (tp-100) REVERT: A 576 ASP cc_start: 0.8844 (t0) cc_final: 0.8067 (m-30) REVERT: A 636 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8433 (tp30) REVERT: A 696 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8588 (tp) REVERT: A 716 MET cc_start: 0.4845 (pmm) cc_final: 0.4569 (pmm) REVERT: C 423 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8802 (tm-30) REVERT: C 445 MET cc_start: 0.9386 (tpp) cc_final: 0.9056 (tpp) REVERT: C 561 GLN cc_start: 0.8319 (mp10) cc_final: 0.8020 (mp10) REVERT: C 576 ASP cc_start: 0.8912 (t0) cc_final: 0.7894 (m-30) REVERT: C 593 THR cc_start: 0.9503 (m) cc_final: 0.9268 (t) REVERT: C 668 ILE cc_start: 0.9301 (mt) cc_final: 0.9094 (mp) REVERT: D 504 LYS cc_start: 0.8493 (mttp) cc_final: 0.8273 (mttp) REVERT: D 509 ASP cc_start: 0.8501 (p0) cc_final: 0.8285 (p0) REVERT: D 536 GLU cc_start: 0.8502 (mp0) cc_final: 0.8210 (mp0) REVERT: D 561 GLN cc_start: 0.8238 (mp10) cc_final: 0.7906 (mp10) REVERT: D 576 ASP cc_start: 0.8947 (t0) cc_final: 0.8032 (m-30) REVERT: D 636 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8383 (tp30) REVERT: D 668 ILE cc_start: 0.9209 (mt) cc_final: 0.8995 (mp) REVERT: B 503 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8757 (tt) REVERT: B 576 ASP cc_start: 0.8951 (t0) cc_final: 0.8128 (m-30) REVERT: B 677 MET cc_start: 0.8566 (ttp) cc_final: 0.8261 (tmm) REVERT: E 34 TYR cc_start: 0.7185 (m-80) cc_final: 0.6960 (m-80) REVERT: E 47 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8452 (mm-30) REVERT: E 68 ILE cc_start: 0.9439 (mt) cc_final: 0.9103 (pt) REVERT: F 21 PHE cc_start: 0.7071 (m-10) cc_final: 0.6815 (m-10) REVERT: F 34 TYR cc_start: 0.7540 (m-80) cc_final: 0.7135 (m-10) REVERT: F 47 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8760 (mm-30) REVERT: F 68 ILE cc_start: 0.9365 (mt) cc_final: 0.9067 (pt) outliers start: 64 outliers final: 46 residues processed: 394 average time/residue: 0.2470 time to fit residues: 147.9780 Evaluate side-chains 399 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 351 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 164 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16392 Z= 0.209 Angle : 0.537 11.417 22224 Z= 0.280 Chirality : 0.038 0.137 2472 Planarity : 0.003 0.048 2724 Dihedral : 5.693 39.888 2511 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.25 % Allowed : 15.75 % Favored : 80.00 % 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: 0.49 (0.20), residues: 1914 helix: 1.93 (0.17), residues: 1000 sheet: 0.90 (0.74), residues: 64 loop : -1.81 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 740 HIS 0.008 0.001 HIS D 289 PHE 0.024 0.001 PHE C 580 TYR 0.012 0.001 TYR C 584 ARG 0.002 0.000 ARG C 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 359 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.9285 (tp40) cc_final: 0.8896 (tp-100) REVERT: A 562 MET cc_start: 0.7561 (mtt) cc_final: 0.7200 (mtt) REVERT: A 576 ASP cc_start: 0.8973 (t0) cc_final: 0.8113 (m-30) REVERT: A 696 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8578 (tp) REVERT: C 423 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8808 (tm-30) REVERT: C 503 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8840 (tt) REVERT: C 561 GLN cc_start: 0.8329 (mp10) cc_final: 0.8010 (mp10) REVERT: C 575 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7499 (ttp80) REVERT: C 576 ASP cc_start: 0.8951 (t0) cc_final: 0.7903 (m-30) REVERT: D 445 MET cc_start: 0.9271 (tpp) cc_final: 0.9036 (tpp) REVERT: D 503 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8791 (tt) REVERT: D 561 GLN cc_start: 0.8188 (mp10) cc_final: 0.7856 (mp10) REVERT: D 576 ASP cc_start: 0.8953 (t0) cc_final: 0.8247 (m-30) REVERT: D 636 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8462 (tp30) REVERT: B 445 MET cc_start: 0.9332 (tpp) cc_final: 0.8981 (tpp) REVERT: B 576 ASP cc_start: 0.8949 (t0) cc_final: 0.8044 (m-30) REVERT: B 677 MET cc_start: 0.8642 (ttp) cc_final: 0.8336 (tmm) REVERT: E 17 ASP cc_start: 0.7275 (t0) cc_final: 0.6931 (t0) REVERT: E 34 TYR cc_start: 0.7242 (m-80) cc_final: 0.6863 (m-10) REVERT: E 47 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8471 (mm-30) REVERT: E 68 ILE cc_start: 0.9451 (mt) cc_final: 0.9134 (pt) REVERT: F 21 PHE cc_start: 0.7131 (m-10) cc_final: 0.6817 (m-10) REVERT: F 34 TYR cc_start: 0.7591 (m-80) cc_final: 0.7108 (m-10) REVERT: F 47 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8700 (mm-30) REVERT: F 68 ILE cc_start: 0.9363 (mt) cc_final: 0.9092 (pt) outliers start: 74 outliers final: 54 residues processed: 383 average time/residue: 0.2428 time to fit residues: 141.3968 Evaluate side-chains 400 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 342 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 183 optimal weight: 0.0070 chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 15 optimal weight: 0.0000 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 overall best weight: 1.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16392 Z= 0.160 Angle : 0.511 12.240 22224 Z= 0.266 Chirality : 0.038 0.148 2472 Planarity : 0.003 0.046 2724 Dihedral : 5.503 42.701 2511 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.08 % Allowed : 16.38 % Favored : 79.54 % 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: 0.73 (0.20), residues: 1914 helix: 2.14 (0.17), residues: 980 sheet: 0.96 (0.74), residues: 64 loop : -1.63 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 697 HIS 0.007 0.001 HIS D 289 PHE 0.030 0.001 PHE C 580 TYR 0.010 0.001 TYR C 584 ARG 0.001 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 370 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASP cc_start: 0.8038 (m-30) cc_final: 0.7823 (m-30) REVERT: A 423 GLN cc_start: 0.9280 (tp40) cc_final: 0.8904 (tp-100) REVERT: A 576 ASP cc_start: 0.8971 (t0) cc_final: 0.8115 (m-30) REVERT: A 696 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 716 MET cc_start: 0.4285 (pmm) cc_final: 0.3821 (pmm) REVERT: C 423 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 445 MET cc_start: 0.9366 (tpp) cc_final: 0.9125 (tpp) REVERT: C 503 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8824 (tt) REVERT: C 561 GLN cc_start: 0.8258 (mp10) cc_final: 0.7970 (mp10) REVERT: C 576 ASP cc_start: 0.8899 (t0) cc_final: 0.7788 (m-30) REVERT: D 445 MET cc_start: 0.9266 (tpp) cc_final: 0.8912 (tpp) REVERT: D 503 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8779 (tt) REVERT: D 561 GLN cc_start: 0.8248 (mp10) cc_final: 0.7923 (mp10) REVERT: D 576 ASP cc_start: 0.8953 (t0) cc_final: 0.8122 (m-30) REVERT: D 636 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8401 (tp30) REVERT: B 359 GLU cc_start: 0.4302 (tt0) cc_final: 0.3922 (tm-30) REVERT: B 418 LEU cc_start: 0.8362 (mp) cc_final: 0.8150 (pt) REVERT: B 445 MET cc_start: 0.9349 (tpp) cc_final: 0.8886 (tpp) REVERT: B 576 ASP cc_start: 0.8984 (t0) cc_final: 0.8126 (m-30) REVERT: B 677 MET cc_start: 0.8615 (ttp) cc_final: 0.8291 (tmm) REVERT: E 34 TYR cc_start: 0.7394 (m-80) cc_final: 0.7054 (m-10) REVERT: E 47 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8516 (mm-30) REVERT: E 68 ILE cc_start: 0.9462 (mt) cc_final: 0.9142 (pt) REVERT: F 14 LYS cc_start: 0.8102 (ptmt) cc_final: 0.7694 (ptpp) REVERT: F 21 PHE cc_start: 0.7188 (m-10) cc_final: 0.6716 (m-10) REVERT: F 34 TYR cc_start: 0.7611 (m-80) cc_final: 0.7009 (m-80) REVERT: F 47 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8697 (mm-30) REVERT: F 68 ILE cc_start: 0.9360 (mt) cc_final: 0.9101 (pt) REVERT: F 72 GLU cc_start: 0.6658 (pp20) cc_final: 0.6385 (pp20) outliers start: 71 outliers final: 56 residues processed: 396 average time/residue: 0.2651 time to fit residues: 161.2785 Evaluate side-chains 407 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 348 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain D residue 339 LEU 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 503 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16392 Z= 0.158 Angle : 0.532 10.396 22224 Z= 0.277 Chirality : 0.038 0.158 2472 Planarity : 0.003 0.045 2724 Dihedral : 5.489 51.232 2511 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.62 % Allowed : 17.82 % Favored : 78.56 % 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: 0.72 (0.20), residues: 1914 helix: 2.09 (0.17), residues: 984 sheet: 1.04 (0.75), residues: 64 loop : -1.59 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 697 HIS 0.010 0.001 HIS B 289 PHE 0.028 0.001 PHE C 580 TYR 0.009 0.001 TYR C 584 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 373 time to evaluate : 1.944 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: A 411 ASP cc_start: 0.8008 (m-30) cc_final: 0.7805 (m-30) REVERT: A 423 GLN cc_start: 0.9281 (tp40) cc_final: 0.8888 (tp-100) REVERT: A 445 MET cc_start: 0.9232 (tpp) cc_final: 0.8919 (tpp) REVERT: A 472 TYR cc_start: 0.8196 (m-80) cc_final: 0.7835 (m-80) REVERT: A 562 MET cc_start: 0.7556 (mtt) cc_final: 0.7211 (mtt) REVERT: A 576 ASP cc_start: 0.8929 (t0) cc_final: 0.7976 (m-30) REVERT: A 636 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8372 (tp30) REVERT: A 716 MET cc_start: 0.4306 (pmm) cc_final: 0.3877 (pmm) REVERT: C 423 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8806 (tm-30) REVERT: C 445 MET cc_start: 0.9354 (tpp) cc_final: 0.9028 (tpp) REVERT: C 503 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8845 (tt) REVERT: C 561 GLN cc_start: 0.8190 (mp10) cc_final: 0.7912 (mp10) REVERT: C 575 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7497 (ttp80) REVERT: C 576 ASP cc_start: 0.8927 (t0) cc_final: 0.7767 (m-30) REVERT: D 503 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8783 (tt) REVERT: D 561 GLN cc_start: 0.8243 (mp10) cc_final: 0.7929 (mp10) REVERT: D 576 ASP cc_start: 0.8978 (t0) cc_final: 0.8152 (m-30) REVERT: D 636 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8348 (tp30) REVERT: B 359 GLU cc_start: 0.4282 (tt0) cc_final: 0.3901 (tm-30) REVERT: B 418 LEU cc_start: 0.8369 (mp) cc_final: 0.8144 (pt) REVERT: B 576 ASP cc_start: 0.8980 (t0) cc_final: 0.7938 (m-30) REVERT: B 677 MET cc_start: 0.8616 (ttp) cc_final: 0.8293 (tmm) REVERT: E 34 TYR cc_start: 0.7383 (m-80) cc_final: 0.7043 (m-10) REVERT: E 47 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8455 (mm-30) REVERT: E 68 ILE cc_start: 0.9485 (mt) cc_final: 0.9172 (pt) REVERT: F 14 LYS cc_start: 0.8064 (ptmt) cc_final: 0.7667 (ptpp) REVERT: F 21 PHE cc_start: 0.7260 (m-10) cc_final: 0.6821 (m-10) REVERT: F 34 TYR cc_start: 0.7598 (m-80) cc_final: 0.7057 (m-80) REVERT: F 47 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8663 (mm-30) REVERT: F 68 ILE cc_start: 0.9361 (mt) cc_final: 0.9118 (pt) outliers start: 63 outliers final: 51 residues processed: 400 average time/residue: 0.2543 time to fit residues: 154.8622 Evaluate side-chains 402 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 348 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU 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 503 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16392 Z= 0.215 Angle : 0.555 9.561 22224 Z= 0.291 Chirality : 0.039 0.150 2472 Planarity : 0.003 0.045 2724 Dihedral : 5.681 58.136 2511 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.74 % Allowed : 17.99 % Favored : 78.28 % 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: 0.51 (0.20), residues: 1914 helix: 1.88 (0.17), residues: 1004 sheet: 1.03 (0.75), residues: 64 loop : -1.73 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 53 HIS 0.011 0.001 HIS B 289 PHE 0.027 0.001 PHE C 580 TYR 0.011 0.001 TYR C 584 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 364 time to evaluate : 1.830 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: A 411 ASP cc_start: 0.7871 (m-30) cc_final: 0.7506 (m-30) REVERT: A 423 GLN cc_start: 0.9281 (tp40) cc_final: 0.8880 (tp-100) REVERT: A 472 TYR cc_start: 0.8132 (m-80) cc_final: 0.7735 (m-80) REVERT: A 576 ASP cc_start: 0.8874 (t0) cc_final: 0.7886 (m-30) REVERT: A 700 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8387 (mp10) REVERT: A 716 MET cc_start: 0.3759 (pmm) cc_final: 0.3323 (pmm) REVERT: C 420 ARG cc_start: 0.9029 (mmm-85) cc_final: 0.8171 (mmm160) REVERT: C 423 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8799 (tm-30) REVERT: C 503 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8862 (tt) REVERT: C 561 GLN cc_start: 0.8231 (mp10) cc_final: 0.7944 (mp10) REVERT: C 575 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7433 (ttp80) REVERT: D 576 ASP cc_start: 0.8947 (t0) cc_final: 0.8114 (m-30) REVERT: B 409 ARG cc_start: 0.8507 (ptm160) cc_final: 0.7918 (ttp-170) REVERT: B 445 MET cc_start: 0.9276 (tpp) cc_final: 0.9017 (tpp) REVERT: B 576 ASP cc_start: 0.8994 (t0) cc_final: 0.8135 (m-30) REVERT: B 636 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8352 (tp30) REVERT: B 677 MET cc_start: 0.8642 (ttp) cc_final: 0.8282 (tmm) REVERT: E 34 TYR cc_start: 0.7407 (m-80) cc_final: 0.7110 (m-10) REVERT: E 47 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8350 (mm-30) REVERT: E 68 ILE cc_start: 0.9453 (mt) cc_final: 0.9099 (pt) REVERT: F 14 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7812 (ptpp) REVERT: F 21 PHE cc_start: 0.7360 (m-10) cc_final: 0.6900 (m-10) REVERT: F 34 TYR cc_start: 0.7658 (m-80) cc_final: 0.7102 (m-80) REVERT: F 47 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8447 (mm-30) REVERT: F 68 ILE cc_start: 0.9380 (mt) cc_final: 0.9132 (pt) REVERT: F 72 GLU cc_start: 0.6351 (pp20) cc_final: 0.6113 (pp20) outliers start: 65 outliers final: 61 residues processed: 388 average time/residue: 0.2457 time to fit residues: 144.2880 Evaluate side-chains 405 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 342 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 707 ASP Chi-restraints excluded: chain D residue 737 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16392 Z= 0.164 Angle : 0.565 14.153 22224 Z= 0.291 Chirality : 0.038 0.172 2472 Planarity : 0.003 0.044 2724 Dihedral : 5.500 55.287 2511 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.51 % Allowed : 18.62 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1914 helix: 2.13 (0.17), residues: 984 sheet: 1.10 (0.76), residues: 64 loop : -1.73 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 697 HIS 0.011 0.001 HIS B 289 PHE 0.026 0.001 PHE A 304 TYR 0.010 0.001 TYR B 401 ARG 0.005 0.000 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 372 time to evaluate : 1.983 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 423 GLN cc_start: 0.9281 (tp40) cc_final: 0.8881 (tp-100) REVERT: A 472 TYR cc_start: 0.8157 (m-80) cc_final: 0.7780 (m-80) REVERT: A 576 ASP cc_start: 0.8848 (t0) cc_final: 0.7904 (m-30) REVERT: A 700 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8458 (mp10) REVERT: C 423 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8783 (tm-30) REVERT: C 503 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8831 (tt) REVERT: C 561 GLN cc_start: 0.8219 (mp10) cc_final: 0.7915 (mp10) REVERT: C 575 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7389 (ttp80) REVERT: C 677 MET cc_start: 0.8657 (ttp) cc_final: 0.8382 (ttp) REVERT: D 499 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8209 (tpp-160) REVERT: D 576 ASP cc_start: 0.8962 (t0) cc_final: 0.8180 (m-30) REVERT: D 636 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8332 (tp30) REVERT: D 700 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8457 (mp10) REVERT: B 409 ARG cc_start: 0.8703 (ptm160) cc_final: 0.7993 (ttp-170) REVERT: B 445 MET cc_start: 0.9243 (tpp) cc_final: 0.8980 (tpp) REVERT: B 499 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8237 (tpp-160) REVERT: B 576 ASP cc_start: 0.8979 (t0) cc_final: 0.8152 (m-30) REVERT: B 677 MET cc_start: 0.8592 (ttp) cc_final: 0.8215 (tmm) REVERT: E 34 TYR cc_start: 0.7455 (m-80) cc_final: 0.7246 (m-10) REVERT: E 47 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8291 (mm-30) REVERT: E 68 ILE cc_start: 0.9463 (mt) cc_final: 0.9185 (pt) REVERT: F 5 GLU cc_start: 0.8789 (tt0) cc_final: 0.8355 (tp30) REVERT: F 14 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7635 (ptpp) REVERT: F 21 PHE cc_start: 0.7345 (m-10) cc_final: 0.6855 (m-10) REVERT: F 34 TYR cc_start: 0.7650 (m-80) cc_final: 0.7179 (m-80) REVERT: F 47 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8594 (mm-30) outliers start: 61 outliers final: 52 residues processed: 396 average time/residue: 0.2575 time to fit residues: 153.7347 Evaluate side-chains 416 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 362 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 592 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 189 optimal weight: 0.0870 chunk 174 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16392 Z= 0.171 Angle : 0.566 11.333 22224 Z= 0.296 Chirality : 0.039 0.185 2472 Planarity : 0.003 0.044 2724 Dihedral : 5.381 48.403 2511 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.45 % Allowed : 19.37 % Favored : 77.18 % 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: 0.67 (0.20), residues: 1914 helix: 2.01 (0.17), residues: 1012 sheet: 1.09 (0.76), residues: 64 loop : -1.70 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 53 HIS 0.011 0.001 HIS B 289 PHE 0.024 0.001 PHE C 580 TYR 0.009 0.001 TYR C 584 ARG 0.003 0.000 ARG C 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3828 Ramachandran restraints generated. 1914 Oldfield, 0 Emsley, 1914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 366 time to evaluate : 1.867 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 423 GLN cc_start: 0.9266 (tp40) cc_final: 0.8851 (tp-100) REVERT: A 472 TYR cc_start: 0.8210 (m-80) cc_final: 0.7823 (m-80) REVERT: A 576 ASP cc_start: 0.8853 (t0) cc_final: 0.7892 (m-30) REVERT: A 700 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8471 (mp10) REVERT: C 423 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8801 (tm-30) REVERT: C 445 MET cc_start: 0.9061 (tpp) cc_final: 0.8848 (tpp) REVERT: C 503 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8844 (tt) REVERT: C 561 GLN cc_start: 0.8190 (mp10) cc_final: 0.7891 (mp10) REVERT: C 575 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7435 (ttp80) REVERT: D 409 ARG cc_start: 0.8589 (ptm160) cc_final: 0.7842 (ttp-110) REVERT: D 636 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8328 (tp30) REVERT: D 700 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8454 (mp10) REVERT: B 445 MET cc_start: 0.9242 (tpp) cc_final: 0.8971 (tpp) REVERT: B 677 MET cc_start: 0.8606 (ttp) cc_final: 0.8349 (ttp) REVERT: E 47 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8534 (mm-30) REVERT: E 68 ILE cc_start: 0.9470 (mt) cc_final: 0.9192 (pt) REVERT: F 5 GLU cc_start: 0.8744 (tt0) cc_final: 0.8410 (tp30) REVERT: F 14 LYS cc_start: 0.7904 (ptmt) cc_final: 0.7611 (ptpp) REVERT: F 32 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7714 (tptt) REVERT: F 34 TYR cc_start: 0.7724 (m-80) cc_final: 0.7273 (m-80) REVERT: F 47 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8635 (mm-30) outliers start: 60 outliers final: 54 residues processed: 388 average time/residue: 0.2579 time to fit residues: 150.2340 Evaluate side-chains 409 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 352 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain C residue 700 GLN Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain E residue 2 CYS Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 15 CYS Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 32 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 150 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 27 optimal weight: 0.0870 chunk 132 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.191296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128239 restraints weight = 24081.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124625 restraints weight = 15861.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125558 restraints weight = 12231.569| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 16392 Z= 0.147 Angle : 0.563 9.942 22224 Z= 0.291 Chirality : 0.038 0.190 2472 Planarity : 0.003 0.047 2724 Dihedral : 5.134 42.588 2511 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.93 % Allowed : 20.34 % Favored : 76.72 % 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: 0.75 (0.20), residues: 1914 helix: 2.10 (0.17), residues: 1016 sheet: 1.16 (0.76), residues: 64 loop : -1.72 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 697 HIS 0.012 0.001 HIS B 289 PHE 0.025 0.001 PHE A 304 TYR 0.008 0.001 TYR A 441 ARG 0.003 0.000 ARG D 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.38 seconds wall clock time: 62 minutes 43.95 seconds (3763.95 seconds total)