Starting phenix.real_space_refine on Fri Mar 15 14:20:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/03_2024/8rfh_19121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/03_2024/8rfh_19121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/03_2024/8rfh_19121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/03_2024/8rfh_19121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/03_2024/8rfh_19121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rfh_19121/03_2024/8rfh_19121_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 58 5.16 5 C 7550 2.51 5 N 2032 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 610": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11802 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5874 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696} Chain breaks: 1 Chain: "B" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5874 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.56, per 1000 atoms: 0.56 Number of scatterers: 11802 At special positions: 0 Unit cell: (141.588, 78.66, 91.908, 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 58 16.00 P 4 15.00 O 2158 8.00 N 2032 7.00 C 7550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 2.4 seconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 12 sheets defined 37.7% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.575A pdb=" N LYS A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.943A pdb=" N ILE A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 316 through 327 removed outlier: 3.550A pdb=" N ILE A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 4.111A pdb=" N LEU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 389 through 402 removed outlier: 4.730A pdb=" N ASP A 401 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.688A pdb=" N GLY A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 434 Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 481 through 493 Processing helix chain 'A' and resid 512 through 517 removed outlier: 4.313A pdb=" N THR A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 533 Processing helix chain 'A' and resid 555 through 564 Proline residue: A 559 - end of helix Proline residue: A 562 - end of helix No H-bonds generated for 'chain 'A' and resid 555 through 564' Processing helix chain 'A' and resid 584 through 587 Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 680 through 684 Processing helix chain 'A' and resid 698 through 701 No H-bonds generated for 'chain 'A' and resid 698 through 701' Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 833 through 837 Processing helix chain 'A' and resid 851 through 870 Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 188 through 197 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.575A pdb=" N LYS B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 242 through 255 Processing helix chain 'B' and resid 269 through 278 removed outlier: 3.943A pdb=" N ILE B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 335 through 347 removed outlier: 4.111A pdb=" N LEU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.779A pdb=" N LYS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.687A pdb=" N GLY B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 481 through 493 Processing helix chain 'B' and resid 512 through 517 removed outlier: 4.313A pdb=" N THR B 517 " --> pdb=" O ARG B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 Processing helix chain 'B' and resid 555 through 564 Proline residue: B 559 - end of helix Proline residue: B 562 - end of helix No H-bonds generated for 'chain 'B' and resid 555 through 564' Processing helix chain 'B' and resid 584 through 587 Processing helix chain 'B' and resid 606 through 610 Processing helix chain 'B' and resid 675 through 677 No H-bonds generated for 'chain 'B' and resid 675 through 677' Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 698 through 701 No H-bonds generated for 'chain 'B' and resid 698 through 701' Processing helix chain 'B' and resid 708 through 714 Processing helix chain 'B' and resid 739 through 741 No H-bonds generated for 'chain 'B' and resid 739 through 741' Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 833 through 837 Processing helix chain 'B' and resid 851 through 870 Processing sheet with id= A, first strand: chain 'A' and resid 176 through 181 removed outlier: 6.466A pdb=" N THR A 207 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 262 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 209 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASP A 264 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 211 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 499 through 501 removed outlier: 3.587A pdb=" N GLN A 499 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 522 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 501 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 542 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE A 523 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 544 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 570 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR A 593 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 573 " --> pdb=" O TYR A 593 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA A 595 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER A 575 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER A 597 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN A 577 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 616 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N PHE A 596 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 618 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N SER A 598 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN A 620 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS A 640 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE A 619 " --> pdb=" O HIS A 640 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS A 642 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR A 621 " --> pdb=" O HIS A 642 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 625 through 627 removed outlier: 5.819A pdb=" N SER A 646 " --> pdb=" O LEU A 626 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 843 through 845 removed outlier: 3.715A pdb=" N GLU A 845 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 822 " --> pdb=" O GLU A 845 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 749 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 774 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 752 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 725 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR A 672 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG A 695 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 784 through 786 removed outlier: 6.478A pdb=" N SER A 806 " --> pdb=" O TRP A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 463 through 467 removed outlier: 6.826A pdb=" N THR A 476 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 176 through 181 removed outlier: 6.466A pdb=" N THR B 207 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL B 262 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 209 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASP B 264 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 211 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 499 through 501 removed outlier: 3.585A pdb=" N GLN B 499 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS B 522 " --> pdb=" O GLN B 499 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 501 " --> pdb=" O CYS B 522 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER B 542 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE B 523 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 544 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 570 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR B 593 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 573 " --> pdb=" O TYR B 593 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA B 595 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER B 575 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER B 597 " --> pdb=" O SER B 575 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN B 577 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 616 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N PHE B 596 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 618 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N SER B 598 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN B 620 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS B 640 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE B 619 " --> pdb=" O HIS B 640 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS B 642 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR B 621 " --> pdb=" O HIS B 642 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 625 through 627 removed outlier: 5.820A pdb=" N SER B 646 " --> pdb=" O LEU B 626 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 843 through 845 removed outlier: 3.714A pdb=" N GLU B 845 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 822 " --> pdb=" O GLU B 845 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 749 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 774 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 752 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 725 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 672 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ARG B 695 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 784 through 786 removed outlier: 6.478A pdb=" N SER B 806 " --> pdb=" O TRP B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 463 through 467 removed outlier: 6.828A pdb=" N THR B 476 " --> pdb=" O MET B 466 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 960 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: 4.18 Time building geometry restraints manager: 5.01 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: 3588 1.34 - 1.45: 1609 1.45 - 1.57: 6771 1.57 - 1.69: 6 1.69 - 1.81: 82 Bond restraints: 12056 Sorted by residual: bond pdb=" N THR A 315 " pdb=" CA THR A 315 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.31e-02 5.83e+03 1.08e+01 bond pdb=" N ILE A 673 " pdb=" CA ILE A 673 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N THR B 315 " pdb=" CA THR B 315 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.34e-02 5.57e+03 9.89e+00 bond pdb=" N LEU A 314 " pdb=" CA LEU A 314 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.79e+00 bond pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.15e+00 ... (remaining 12051 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.52: 210 105.52 - 113.12: 6681 113.12 - 120.73: 5335 120.73 - 128.33: 3961 128.33 - 135.93: 99 Bond angle restraints: 16286 Sorted by residual: angle pdb=" C SER A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta sigma weight residual 122.30 114.12 8.18 1.35e+00 5.49e-01 3.67e+01 angle pdb=" C THR A 672 " pdb=" CA THR A 672 " pdb=" CB THR A 672 " ideal model delta sigma weight residual 110.22 120.17 -9.95 1.67e+00 3.59e-01 3.55e+01 angle pdb=" N ASP B 317 " pdb=" CA ASP B 317 " pdb=" C ASP B 317 " ideal model delta sigma weight residual 111.28 105.88 5.40 1.09e+00 8.42e-01 2.46e+01 angle pdb=" N ASP A 317 " pdb=" CA ASP A 317 " pdb=" C ASP A 317 " ideal model delta sigma weight residual 111.28 106.71 4.57 1.09e+00 8.42e-01 1.76e+01 angle pdb=" C GLU A 316 " pdb=" CA GLU A 316 " pdb=" CB GLU A 316 " ideal model delta sigma weight residual 110.79 105.33 5.46 1.66e+00 3.63e-01 1.08e+01 ... (remaining 16281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 7135 34.69 - 69.38: 185 69.38 - 104.07: 12 104.07 - 138.76: 0 138.76 - 173.45: 2 Dihedral angle restraints: 7334 sinusoidal: 3096 harmonic: 4238 Sorted by residual: dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 113.45 -173.45 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 113.42 -173.42 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA SER A 671 " pdb=" C SER A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta harmonic sigma weight residual -180.00 -150.32 -29.68 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 7331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1622 0.078 - 0.156: 182 0.156 - 0.234: 7 0.234 - 0.311: 0 0.311 - 0.389: 1 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA THR A 672 " pdb=" N THR A 672 " pdb=" C THR A 672 " pdb=" CB THR A 672 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA GLU A 316 " pdb=" N GLU A 316 " pdb=" C GLU A 316 " pdb=" CB GLU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 673 " pdb=" N ILE B 673 " pdb=" C ILE B 673 " pdb=" CB ILE B 673 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1809 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 670 " 0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C LEU A 670 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU A 670 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 671 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 670 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C LEU B 670 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 670 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 671 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 671 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C SER A 671 " -0.048 2.00e-02 2.50e+03 pdb=" O SER A 671 " 0.018 2.00e-02 2.50e+03 pdb=" N THR A 672 " 0.016 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 877 2.74 - 3.28: 12622 3.28 - 3.82: 20276 3.82 - 4.36: 23981 4.36 - 4.90: 38564 Nonbonded interactions: 96320 Sorted by model distance: nonbonded pdb=" OG1 THR B 469 " pdb=" OD1 ASP B 471 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR A 469 " pdb=" OD1 ASP A 471 " model vdw 2.201 2.440 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASP A 270 " model vdw 2.280 2.440 nonbonded pdb=" OG SER B 268 " pdb=" OD1 ASP B 270 " model vdw 2.280 2.440 nonbonded pdb=" O VAL A 653 " pdb=" NH2 ARG A 685 " model vdw 2.293 2.520 ... (remaining 96315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.380 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 36.420 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12056 Z= 0.204 Angle : 0.760 11.116 16286 Z= 0.383 Chirality : 0.048 0.389 1812 Planarity : 0.004 0.043 2060 Dihedral : 15.836 173.446 4582 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.69 % Favored : 97.18 % Rotamer: Outliers : 1.44 % Allowed : 21.35 % Favored : 77.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.03 % 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: 0.66 (0.23), residues: 1452 helix: 0.50 (0.23), residues: 518 sheet: 0.20 (0.37), residues: 212 loop : 0.67 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 798 HIS 0.004 0.001 HIS A 524 PHE 0.010 0.001 PHE B 571 TYR 0.006 0.001 TYR B 413 ARG 0.007 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.431 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 351 LEU cc_start: 0.7900 (tt) cc_final: 0.7248 (tp) REVERT: A 456 ASP cc_start: 0.8905 (m-30) cc_final: 0.8319 (t70) REVERT: A 692 LEU cc_start: 0.9270 (tp) cc_final: 0.9021 (tp) REVERT: A 844 MET cc_start: 0.7277 (tmm) cc_final: 0.7032 (tmm) REVERT: B 351 LEU cc_start: 0.7779 (tt) cc_final: 0.7215 (tp) REVERT: B 432 TRP cc_start: 0.8378 (m-10) cc_final: 0.8029 (m-90) REVERT: B 456 ASP cc_start: 0.8881 (m-30) cc_final: 0.8274 (t70) REVERT: B 671 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6842 (p) REVERT: B 672 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6154 (p) REVERT: B 692 LEU cc_start: 0.9234 (tp) cc_final: 0.9018 (tp) REVERT: B 844 MET cc_start: 0.7143 (tmm) cc_final: 0.6898 (tmm) outliers start: 19 outliers final: 3 residues processed: 194 average time/residue: 0.2030 time to fit residues: 59.3351 Evaluate side-chains 172 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 672 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 40.0000 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 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 349 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 GLN B 309 HIS B 349 ASN B 668 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12056 Z= 0.155 Angle : 0.629 10.665 16286 Z= 0.289 Chirality : 0.043 0.149 1812 Planarity : 0.004 0.043 2060 Dihedral : 7.259 146.550 1586 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.96 % Allowed : 18.47 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.23), residues: 1452 helix: 0.71 (0.24), residues: 518 sheet: 0.14 (0.38), residues: 202 loop : 0.59 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 432 HIS 0.003 0.001 HIS B 539 PHE 0.014 0.001 PHE A 585 TYR 0.012 0.001 TYR A 259 ARG 0.004 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 ASP cc_start: 0.8913 (m-30) cc_final: 0.8362 (t70) REVERT: A 671 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7185 (p) REVERT: A 736 LEU cc_start: 0.9112 (mm) cc_final: 0.8906 (mm) REVERT: A 844 MET cc_start: 0.7406 (tmm) cc_final: 0.7178 (tmm) REVERT: B 313 PHE cc_start: 0.7863 (m-80) cc_final: 0.7525 (m-80) REVERT: B 432 TRP cc_start: 0.8421 (m-10) cc_final: 0.8159 (m-90) REVERT: B 671 SER cc_start: 0.8008 (t) cc_final: 0.7648 (p) REVERT: B 736 LEU cc_start: 0.9007 (mm) cc_final: 0.8774 (mm) REVERT: B 841 PHE cc_start: 0.8755 (t80) cc_final: 0.8542 (t80) outliers start: 39 outliers final: 20 residues processed: 193 average time/residue: 0.1944 time to fit residues: 59.4374 Evaluate side-chains 184 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 775 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 132 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 455 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12056 Z= 0.351 Angle : 0.729 9.934 16286 Z= 0.357 Chirality : 0.047 0.154 1812 Planarity : 0.005 0.048 2060 Dihedral : 6.909 122.851 1583 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.65 % Allowed : 17.78 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.59 (0.23), residues: 1452 helix: 0.82 (0.24), residues: 488 sheet: -0.22 (0.37), residues: 198 loop : 0.45 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 432 HIS 0.007 0.002 HIS B 309 PHE 0.020 0.002 PHE A 530 TYR 0.018 0.002 TYR A 212 ARG 0.005 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 ILE cc_start: 0.9220 (pp) cc_final: 0.9011 (pp) REVERT: A 522 CYS cc_start: 0.7530 (p) cc_final: 0.7272 (p) REVERT: B 313 PHE cc_start: 0.8066 (m-80) cc_final: 0.7719 (m-80) REVERT: B 351 LEU cc_start: 0.7591 (tt) cc_final: 0.7013 (tp) REVERT: B 407 LEU cc_start: 0.9577 (tp) cc_final: 0.9354 (tp) REVERT: B 522 CYS cc_start: 0.7475 (p) cc_final: 0.7205 (p) REVERT: B 671 SER cc_start: 0.8283 (t) cc_final: 0.8080 (p) outliers start: 48 outliers final: 35 residues processed: 190 average time/residue: 0.1943 time to fit residues: 57.1198 Evaluate side-chains 193 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12056 Z= 0.355 Angle : 0.720 10.078 16286 Z= 0.351 Chirality : 0.047 0.228 1812 Planarity : 0.005 0.047 2060 Dihedral : 6.743 108.396 1582 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.26 % Allowed : 19.15 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.27 (0.23), residues: 1452 helix: 0.64 (0.23), residues: 490 sheet: -0.60 (0.36), residues: 198 loop : 0.25 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 432 HIS 0.008 0.002 HIS A 309 PHE 0.019 0.002 PHE A 530 TYR 0.013 0.002 TYR B 413 ARG 0.004 0.001 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 1.433 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 407 LEU cc_start: 0.9582 (tp) cc_final: 0.9265 (tp) REVERT: A 429 ILE cc_start: 0.9243 (pp) cc_final: 0.9033 (pp) REVERT: A 432 TRP cc_start: 0.8271 (m-90) cc_final: 0.8023 (m-90) REVERT: A 522 CYS cc_start: 0.7612 (p) cc_final: 0.7300 (p) REVERT: B 313 PHE cc_start: 0.8183 (m-80) cc_final: 0.7760 (m-80) REVERT: B 522 CYS cc_start: 0.7645 (p) cc_final: 0.7362 (p) outliers start: 56 outliers final: 41 residues processed: 196 average time/residue: 0.1882 time to fit residues: 56.8800 Evaluate side-chains 200 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 120 optimal weight: 0.0000 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12056 Z= 0.221 Angle : 0.679 10.836 16286 Z= 0.315 Chirality : 0.045 0.312 1812 Planarity : 0.004 0.054 2060 Dihedral : 6.261 91.806 1582 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.04 % Allowed : 20.82 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.23), residues: 1452 helix: 0.80 (0.24), residues: 478 sheet: -0.40 (0.37), residues: 182 loop : 0.18 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 432 HIS 0.005 0.001 HIS A 309 PHE 0.019 0.002 PHE B 571 TYR 0.009 0.001 TYR B 413 ARG 0.004 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 1.501 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 403 LEU cc_start: 0.8415 (tp) cc_final: 0.7970 (tp) REVERT: B 522 CYS cc_start: 0.7583 (p) cc_final: 0.7310 (p) REVERT: B 740 TYR cc_start: 0.8881 (p90) cc_final: 0.8649 (p90) outliers start: 40 outliers final: 29 residues processed: 197 average time/residue: 0.1977 time to fit residues: 59.0358 Evaluate side-chains 199 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12056 Z= 0.170 Angle : 0.694 13.150 16286 Z= 0.310 Chirality : 0.045 0.322 1812 Planarity : 0.004 0.056 2060 Dihedral : 5.924 81.815 1582 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.36 % Allowed : 21.66 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.48 (0.23), residues: 1452 helix: 0.80 (0.25), residues: 480 sheet: -0.13 (0.36), residues: 190 loop : 0.28 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 432 HIS 0.005 0.001 HIS A 524 PHE 0.018 0.001 PHE A 571 TYR 0.008 0.001 TYR A 740 ARG 0.005 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.368 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 351 LEU cc_start: 0.7313 (tp) cc_final: 0.7112 (tt) REVERT: B 323 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8645 (pp) REVERT: B 351 LEU cc_start: 0.7285 (tt) cc_final: 0.6910 (tt) REVERT: B 403 LEU cc_start: 0.8202 (mm) cc_final: 0.7999 (mp) REVERT: B 740 TYR cc_start: 0.8862 (p90) cc_final: 0.8618 (p90) outliers start: 31 outliers final: 20 residues processed: 195 average time/residue: 0.1969 time to fit residues: 58.4133 Evaluate side-chains 190 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 775 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 118 optimal weight: 0.0060 chunk 78 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12056 Z= 0.179 Angle : 0.699 15.305 16286 Z= 0.315 Chirality : 0.045 0.291 1812 Planarity : 0.004 0.056 2060 Dihedral : 5.785 76.417 1582 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.74 % Allowed : 22.26 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.48 (0.23), residues: 1452 helix: 0.80 (0.24), residues: 480 sheet: -0.08 (0.36), residues: 190 loop : 0.26 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP A 432 HIS 0.004 0.001 HIS A 524 PHE 0.027 0.001 PHE B 841 TYR 0.007 0.001 TYR A 740 ARG 0.004 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.325 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 403 LEU cc_start: 0.8500 (tp) cc_final: 0.8251 (tt) REVERT: A 410 CYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9052 (p) REVERT: B 403 LEU cc_start: 0.8178 (mm) cc_final: 0.7974 (mp) REVERT: B 740 TYR cc_start: 0.8846 (p90) cc_final: 0.8599 (p90) outliers start: 36 outliers final: 27 residues processed: 200 average time/residue: 0.1873 time to fit residues: 57.8661 Evaluate side-chains 198 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12056 Z= 0.189 Angle : 0.713 15.416 16286 Z= 0.320 Chirality : 0.046 0.322 1812 Planarity : 0.004 0.056 2060 Dihedral : 5.727 70.452 1582 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.66 % Allowed : 22.26 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.47 (0.23), residues: 1452 helix: 0.82 (0.25), residues: 480 sheet: -0.17 (0.36), residues: 190 loop : 0.25 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.002 TRP A 432 HIS 0.004 0.001 HIS A 524 PHE 0.013 0.001 PHE A 571 TYR 0.007 0.001 TYR A 740 ARG 0.004 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.443 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 351 LEU cc_start: 0.7754 (tt) cc_final: 0.7168 (tp) REVERT: A 403 LEU cc_start: 0.8622 (tp) cc_final: 0.8376 (tt) REVERT: A 410 CYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9030 (p) REVERT: B 323 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8667 (pp) REVERT: B 403 LEU cc_start: 0.8227 (mm) cc_final: 0.7979 (mp) REVERT: B 740 TYR cc_start: 0.8839 (p90) cc_final: 0.8599 (p90) REVERT: B 767 MET cc_start: 0.7720 (tpp) cc_final: 0.7423 (tpp) outliers start: 35 outliers final: 30 residues processed: 185 average time/residue: 0.1850 time to fit residues: 52.9083 Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 874 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS A 778 ASN B 769 HIS B 778 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12056 Z= 0.310 Angle : 0.768 15.216 16286 Z= 0.360 Chirality : 0.048 0.366 1812 Planarity : 0.005 0.054 2060 Dihedral : 6.030 69.901 1582 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.42 % Allowed : 22.26 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.31 (0.23), residues: 1452 helix: 0.68 (0.24), residues: 500 sheet: -0.44 (0.36), residues: 190 loop : 0.21 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.003 TRP A 432 HIS 0.005 0.001 HIS A 309 PHE 0.016 0.002 PHE A 841 TYR 0.016 0.002 TYR B 259 ARG 0.003 0.000 ARG B 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7623 (tt) cc_final: 0.7025 (tp) REVERT: A 403 LEU cc_start: 0.8704 (tp) cc_final: 0.8340 (tt) REVERT: A 410 CYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9175 (p) REVERT: B 323 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8704 (pp) REVERT: B 403 LEU cc_start: 0.8262 (mm) cc_final: 0.8003 (mp) REVERT: B 522 CYS cc_start: 0.7677 (p) cc_final: 0.7315 (p) REVERT: B 572 ASP cc_start: 0.8313 (t0) cc_final: 0.8082 (t0) outliers start: 45 outliers final: 37 residues processed: 193 average time/residue: 0.2090 time to fit residues: 61.6266 Evaluate side-chains 202 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 875 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 96 optimal weight: 0.0670 chunk 145 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12056 Z= 0.180 Angle : 0.738 16.218 16286 Z= 0.332 Chirality : 0.046 0.401 1812 Planarity : 0.004 0.056 2060 Dihedral : 5.676 58.352 1580 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.20 % Allowed : 23.56 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.36 (0.23), residues: 1452 helix: 0.73 (0.24), residues: 482 sheet: -0.38 (0.36), residues: 190 loop : 0.24 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.002 TRP A 432 HIS 0.010 0.001 HIS A 539 PHE 0.013 0.001 PHE A 571 TYR 0.016 0.001 TYR B 259 ARG 0.003 0.000 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7548 (tt) cc_final: 0.6985 (tp) REVERT: A 403 LEU cc_start: 0.8774 (tp) cc_final: 0.8446 (tt) REVERT: B 323 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8713 (pp) REVERT: B 403 LEU cc_start: 0.8177 (mm) cc_final: 0.7948 (mp) outliers start: 29 outliers final: 26 residues processed: 193 average time/residue: 0.2072 time to fit residues: 61.2305 Evaluate side-chains 196 residues out of total 1316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 874 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.104428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075941 restraints weight = 34796.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.078954 restraints weight = 19067.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.080985 restraints weight = 13068.502| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12056 Z= 0.171 Angle : 0.736 16.794 16286 Z= 0.328 Chirality : 0.046 0.403 1812 Planarity : 0.004 0.055 2060 Dihedral : 5.559 57.276 1580 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.20 % Allowed : 23.33 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.23), residues: 1452 helix: 0.77 (0.24), residues: 480 sheet: -0.34 (0.35), residues: 212 loop : 0.28 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.133 0.002 TRP A 432 HIS 0.008 0.001 HIS A 539 PHE 0.020 0.001 PHE A 841 TYR 0.014 0.001 TYR B 259 ARG 0.004 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.28 seconds wall clock time: 43 minutes 28.43 seconds (2608.43 seconds total)