Starting phenix.real_space_refine (version: dev) on Tue Apr 5 21:20:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/04_2022/7l2m_23133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/04_2022/7l2m_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_23133/04_2022/7l2m_23133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/04_2022/7l2m_23133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/04_2022/7l2m_23133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2m_23133/04_2022/7l2m_23133_updated.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 10, 'TRANS': 434, 'PCIS': 1} 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: {'PTRANS': 10, 'TRANS': 434, 'PCIS': 1} 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: {'PTRANS': 10, 'TRANS': 434, 'PCIS': 1} 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: {'PTRANS': 10, 'TRANS': 434, 'PCIS': 1} 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: 9.25, per 1000 atoms: 0.58 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: 6.77 Conformation dependent library (CDL) restraints added in 2.5 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: 1.40 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: 4.50 Time building geometry restraints manager: 7.33 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: 9012 17.84 - 35.67: 480 35.67 - 53.51: 89 53.51 - 71.34: 13 71.34 - 89.18: 10 Dihedral angle restraints: 9604 sinusoidal: 3894 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 9601 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 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. 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.120 Process input model: 42.560 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 11.749 89.181 5900 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 % 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 *********************** 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 : 1.922 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 outliers start: 13 outliers final: 6 residues processed: 548 average time/residue: 0.2663 time to fit residues: 215.1482 Evaluate side-chains 346 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 340 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1303 time to fit residues: 4.1676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 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: 9.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 172 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN ** C 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN D 551 ASN D 560 GLN B 410 HIS B 551 ASN B 676 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 16392 Z= 0.166 Angle : 0.550 10.702 22224 Z= 0.287 Chirality : 0.038 0.142 2472 Planarity : 0.004 0.062 2724 Dihedral : 5.935 58.786 2166 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.49 % Favored : 94.41 % Rotamer Outliers : 1.90 % 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: 0.71 (0.20), residues: 1914 helix: 2.04 (0.16), residues: 1036 sheet: 0.46 (0.67), residues: 64 loop : -1.74 (0.21), residues: 814 *********************** 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 455 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 422 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 434 average time/residue: 0.2486 time to fit residues: 162.7470 Evaluate side-chains 363 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 340 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1327 time to fit residues: 8.6368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN C 289 HIS C 551 ASN D 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 16392 Z= 0.177 Angle : 0.528 7.132 22224 Z= 0.280 Chirality : 0.038 0.140 2472 Planarity : 0.005 0.102 2724 Dihedral : 5.608 55.532 2166 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 2.18 % 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: 0.61 (0.20), residues: 1914 helix: 2.05 (0.17), residues: 1012 sheet: 0.71 (0.71), residues: 64 loop : -1.82 (0.20), residues: 838 *********************** 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 400 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 362 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 374 average time/residue: 0.2485 time to fit residues: 141.2847 Evaluate side-chains 344 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 328 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1515 time to fit residues: 6.7485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN A 551 ASN C 408 ASN C 410 HIS D 408 ASN B 494 GLN B 551 ASN B 676 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 16392 Z= 0.291 Angle : 0.606 10.943 22224 Z= 0.313 Chirality : 0.040 0.158 2472 Planarity : 0.005 0.085 2724 Dihedral : 5.554 56.798 2166 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer Outliers : 2.87 % 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: 0.35 (0.20), residues: 1914 helix: 1.78 (0.17), residues: 1016 sheet: 0.76 (0.72), residues: 64 loop : -1.89 (0.20), residues: 834 *********************** 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 408 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 358 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 36 residues processed: 374 average time/residue: 0.2616 time to fit residues: 148.3317 Evaluate side-chains 364 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 328 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1477 time to fit residues: 12.3888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN B 700 GLN F 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 16392 Z= 0.265 Angle : 0.589 9.787 22224 Z= 0.306 Chirality : 0.039 0.166 2472 Planarity : 0.005 0.078 2724 Dihedral : 5.469 54.957 2166 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1914 helix: 1.86 (0.17), residues: 1012 sheet: 0.87 (0.74), residues: 64 loop : -1.94 (0.21), residues: 838 *********************** 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 372 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 338 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 351 average time/residue: 0.2566 time to fit residues: 136.4578 Evaluate side-chains 347 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 331 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1674 time to fit residues: 7.3779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** F 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 16392 Z= 0.174 Angle : 0.543 8.834 22224 Z= 0.285 Chirality : 0.038 0.164 2472 Planarity : 0.004 0.078 2724 Dihedral : 5.269 55.326 2166 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.98 % 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: 0.53 (0.20), residues: 1914 helix: 1.95 (0.17), residues: 1008 sheet: 1.01 (0.75), residues: 64 loop : -1.82 (0.21), residues: 842 *********************** 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 375 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 358 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 363 average time/residue: 0.2487 time to fit residues: 138.1040 Evaluate side-chains 339 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 328 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1872 time to fit residues: 6.2299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 16392 Z= 0.154 Angle : 0.543 8.881 22224 Z= 0.286 Chirality : 0.038 0.147 2472 Planarity : 0.005 0.081 2724 Dihedral : 5.111 53.021 2166 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.80 % 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: 0.51 (0.20), residues: 1914 helix: 1.89 (0.17), residues: 1008 sheet: 1.13 (0.76), residues: 64 loop : -1.77 (0.21), residues: 842 *********************** 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 369 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 355 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 359 average time/residue: 0.2556 time to fit residues: 140.0545 Evaluate side-chains 343 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 333 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1782 time to fit residues: 5.8163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN D 419 ASN ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 16392 Z= 0.267 Angle : 0.606 7.662 22224 Z= 0.317 Chirality : 0.040 0.144 2472 Planarity : 0.005 0.083 2724 Dihedral : 5.215 45.146 2166 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 1.38 % 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: 0.29 (0.20), residues: 1914 helix: 1.65 (0.17), residues: 1020 sheet: 1.02 (0.75), residues: 64 loop : -1.86 (0.21), residues: 830 *********************** 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 366 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 342 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 350 average time/residue: 0.2590 time to fit residues: 137.6268 Evaluate side-chains 333 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 317 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1315 time to fit residues: 6.5750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 154 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4414 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= 0.166 Angle : 0.573 9.222 22224 Z= 0.300 Chirality : 0.038 0.158 2472 Planarity : 0.005 0.087 2724 Dihedral : 5.145 48.576 2166 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 0.52 % 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: 0.45 (0.20), residues: 1914 helix: 1.81 (0.17), residues: 1016 sheet: 1.17 (0.77), residues: 64 loop : -1.80 (0.21), residues: 834 *********************** 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 373 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 364 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 365 average time/residue: 0.2556 time to fit residues: 141.4492 Evaluate side-chains 351 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 346 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1373 time to fit residues: 4.0617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 150 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 551 ASN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 676 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 16392 Z= 0.168 Angle : 0.572 8.798 22224 Z= 0.303 Chirality : 0.039 0.194 2472 Planarity : 0.005 0.102 2724 Dihedral : 5.139 47.652 2166 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer Outliers : 0.29 % 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: 0.41 (0.20), residues: 1914 helix: 1.75 (0.17), residues: 1016 sheet: 1.24 (0.77), residues: 64 loop : -1.79 (0.21), residues: 834 ********************** 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 368 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 363 time to evaluate : 2.198 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 outliers start: 5 outliers final: 2 residues processed: 364 average time/residue: 0.2716 time to fit residues: 150.1844 Evaluate side-chains 349 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 347 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1692 time to fit residues: 3.3239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN D 498 GLN ** B 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.190793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127098 restraints weight = 23782.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124889 restraints weight = 14640.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125703 restraints weight = 11145.917| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 16392 Z= 0.176 Angle : 0.585 9.044 22224 Z= 0.308 Chirality : 0.039 0.180 2472 Planarity : 0.005 0.091 2724 Dihedral : 5.118 46.345 2166 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.23 % 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: 0.40 (0.20), residues: 1914 helix: 1.75 (0.17), residues: 1016 sheet: 1.26 (0.77), residues: 64 loop : -1.81 (0.21), residues: 834 =============================================================================== Job complete usr+sys time: 3224.05 seconds wall clock time: 59 minutes 33.79 seconds (3573.79 seconds total)