Starting phenix.real_space_refine on Sun Mar 17 03:57:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzj_23608/03_2024/7lzj_23608.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzj_23608/03_2024/7lzj_23608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzj_23608/03_2024/7lzj_23608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzj_23608/03_2024/7lzj_23608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzj_23608/03_2024/7lzj_23608.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lzj_23608/03_2024/7lzj_23608.pdb" } resolution = 2.7 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10497 2.51 5 N 2799 2.21 5 O 3228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B GLU 720": "OE1" <-> "OE2" Residue "B ARG 824": "NH1" <-> "NH2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C ARG 824": "NH1" <-> "NH2" Residue "C GLU 890": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16590 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5530 Classifications: {'peptide': 716} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 684} Chain: "B" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5530 Classifications: {'peptide': 716} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 684} Chain: "C" Number of atoms: 5530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5530 Classifications: {'peptide': 716} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 684} Time building chain proxies: 9.21, per 1000 atoms: 0.56 Number of scatterers: 16590 At special positions: 0 Unit cell: (93.975, 94.87, 172.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3228 8.00 N 2799 7.00 C 10497 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: 6.28 Conformation dependent library (CDL) restraints added in 3.3 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3906 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 26 sheets defined 13.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 205 through 211 removed outlier: 3.717A pdb=" N ASN A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.594A pdb=" N GLY A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 561 through 569 removed outlier: 3.822A pdb=" N GLU A 566 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 646 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 662 through 665 Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 887 through 902 removed outlier: 4.233A pdb=" N VAL A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 removed outlier: 3.808A pdb=" N ASP B 198 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 199 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 200 " --> pdb=" O PHE B 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 200' Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.793A pdb=" N ASN B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.598A pdb=" N GLY B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 removed outlier: 3.784A pdb=" N GLU B 566 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 662 through 665 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.558A pdb=" N PHE B 788 " --> pdb=" O PRO B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 827 removed outlier: 3.506A pdb=" N PHE B 827 " --> pdb=" O LEU B 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 823 through 827' Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 887 through 902 removed outlier: 3.895A pdb=" N VAL B 891 " --> pdb=" O GLY B 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 4.030A pdb=" N ASP C 198 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 199 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 200 " --> pdb=" O PHE C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 200' Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.626A pdb=" N ASN C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 301 through 315 Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.676A pdb=" N GLY C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 569 removed outlier: 3.792A pdb=" N GLU C 566 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 653 through 659 Processing helix chain 'C' and resid 662 through 666 removed outlier: 3.517A pdb=" N VAL C 666 " --> pdb=" O LYS C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 775 No H-bonds generated for 'chain 'C' and resid 773 through 775' Processing helix chain 'C' and resid 784 through 788 Processing helix chain 'C' and resid 823 through 827 removed outlier: 3.512A pdb=" N PHE C 827 " --> pdb=" O LEU C 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 823 through 827' Processing helix chain 'C' and resid 862 through 867 Processing helix chain 'C' and resid 887 through 902 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.606A pdb=" N TYR A 264 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.513A pdb=" N PHE A 274 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N CYS A 433 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS A 407 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA A 435 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N TYR A 409 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE A 430 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 537 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLN A 511 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE A 539 " --> pdb=" O GLN A 511 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 513 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.056A pdb=" N THR A 348 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N CYS A 433 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N HIS A 407 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA A 435 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N TYR A 409 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A 466 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS A 433 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ASN A 468 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA A 435 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE A 593 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU A 545 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 595 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 597 " --> pdb=" O ILE A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.193A pdb=" N ILE A 391 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN A 367 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE A 393 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 389 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TYR A 418 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 391 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP A 415 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 444 " --> pdb=" O TRP A 415 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 417 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLU A 446 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 419 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 441 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TYR A 503 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE A 443 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN A 505 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 445 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N CYS A 500 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU A 528 " --> pdb=" O CYS A 500 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA A 577 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER A 527 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL A 579 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 529 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER A 581 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 531 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR A 601 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N TRP A 627 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 602 " --> pdb=" O TRP A 627 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AA6, first strand: chain 'A' and resid 612 through 613 Processing sheet with id=AA7, first strand: chain 'A' and resid 795 through 801 removed outlier: 6.801A pdb=" N VAL A 844 " --> pdb=" O LYS A 750 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 752 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 842 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 754 " --> pdb=" O LYS A 840 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS A 840 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR A 756 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE A 838 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 839 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A 672 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 841 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AA9, first strand: chain 'A' and resid 727 through 732 removed outlier: 4.010A pdb=" N LEU A 727 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE A 768 " --> pdb=" O SER A 780 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 780 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 770 " --> pdb=" O LEU A 778 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.846A pdb=" N SER B 667 " --> pdb=" O TYR B 845 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 845 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU B 669 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 843 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS B 671 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE B 838 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B 757 " --> pdb=" O PHE B 838 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.556A pdb=" N TYR B 264 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.524A pdb=" N PHE B 274 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE B 430 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE B 537 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN B 511 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 539 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 513 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.022A pdb=" N THR B 348 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE B 593 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU B 545 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS B 595 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 597 " --> pdb=" O ILE B 547 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 334 through 336 removed outlier: 6.377A pdb=" N LEU B 334 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 391 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 367 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE B 393 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS B 389 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR B 418 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 391 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP B 415 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE B 444 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE B 417 " --> pdb=" O PHE B 444 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU B 446 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 419 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN B 441 " --> pdb=" O GLN B 501 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N TYR B 503 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE B 443 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLN B 505 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 445 " --> pdb=" O GLN B 505 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N CYS B 500 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 528 " --> pdb=" O CYS B 500 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA B 577 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL B 579 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 530 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER B 581 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR B 532 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR B 601 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP B 627 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 602 " --> pdb=" O TRP B 627 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB7, first strand: chain 'B' and resid 612 through 613 Processing sheet with id=AB8, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AB9, first strand: chain 'B' and resid 727 through 732 removed outlier: 4.057A pdb=" N LEU B 727 " --> pdb=" O PHE B 813 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 811 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 768 " --> pdb=" O SER B 780 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER B 780 " --> pdb=" O ILE B 768 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 770 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 858 through 859 removed outlier: 6.493A pdb=" N ILE C 841 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 672 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 839 " --> pdb=" O ASN C 672 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE C 838 " --> pdb=" O THR C 757 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 757 " --> pdb=" O PHE C 838 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 220 through 223 removed outlier: 3.545A pdb=" N TYR C 263 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.493A pdb=" N PHE C 274 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE C 430 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU C 406 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER C 432 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 408 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE C 466 " --> pdb=" O HIS C 431 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS C 433 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ASN C 468 " --> pdb=" O CYS C 433 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 435 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE C 593 " --> pdb=" O ASP C 543 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU C 545 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS C 595 " --> pdb=" O GLU C 545 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.102A pdb=" N THR C 348 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE C 430 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU C 406 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER C 432 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 408 " --> pdb=" O SER C 432 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE C 430 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 508 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N ILE C 538 " --> pdb=" O SER C 508 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 510 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR C 540 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 512 " --> pdb=" O TYR C 540 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 589 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 334 through 336 removed outlier: 7.205A pdb=" N ILE C 391 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 367 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE C 393 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS C 389 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR C 418 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 391 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP C 415 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE C 444 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE C 417 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLU C 446 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL C 419 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR C 503 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE C 443 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN C 505 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 445 " --> pdb=" O GLN C 505 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 529 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER C 581 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 531 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR C 601 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TRP C 627 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 602 " --> pdb=" O TRP C 627 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 480 through 482 Processing sheet with id=AC7, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AC8, first strand: chain 'C' and resid 727 through 732 removed outlier: 4.011A pdb=" N LEU C 727 " --> pdb=" O PHE C 813 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 768 " --> pdb=" O SER C 780 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C 780 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 770 " --> pdb=" O LEU C 778 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1050 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: 6.88 Time building geometry restraints manager: 6.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3493 1.33 - 1.45: 4330 1.45 - 1.57: 9079 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 17007 Sorted by residual: bond pdb=" C VAL B 688 " pdb=" N PRO B 689 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.12e-02 7.97e+03 2.14e+01 bond pdb=" N VAL C 867 " pdb=" CA VAL C 867 " ideal model delta sigma weight residual 1.460 1.496 -0.036 8.60e-03 1.35e+04 1.72e+01 bond pdb=" C GLU A 855 " pdb=" N PRO A 856 " ideal model delta sigma weight residual 1.329 1.378 -0.048 1.18e-02 7.18e+03 1.68e+01 bond pdb=" N VAL B 688 " pdb=" CA VAL B 688 " ideal model delta sigma weight residual 1.462 1.497 -0.035 9.10e-03 1.21e+04 1.45e+01 bond pdb=" N GLU A 855 " pdb=" CA GLU A 855 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.35e+01 ... (remaining 17002 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.07: 498 107.07 - 113.86: 9079 113.86 - 120.64: 6778 120.64 - 127.42: 6597 127.42 - 134.20: 142 Bond angle restraints: 23094 Sorted by residual: angle pdb=" CA VAL B 688 " pdb=" C VAL B 688 " pdb=" N PRO B 689 " ideal model delta sigma weight residual 117.00 122.06 -5.06 9.50e-01 1.11e+00 2.84e+01 angle pdb=" N ASP B 589 " pdb=" CA ASP B 589 " pdb=" C ASP B 589 " ideal model delta sigma weight residual 111.90 118.90 -7.00 1.32e+00 5.74e-01 2.81e+01 angle pdb=" CA ASN B 438 " pdb=" C ASN B 438 " pdb=" O ASN B 438 " ideal model delta sigma weight residual 120.43 114.72 5.71 1.09e+00 8.42e-01 2.75e+01 angle pdb=" N TYR B 439 " pdb=" CA TYR B 439 " pdb=" C TYR B 439 " ideal model delta sigma weight residual 111.11 117.36 -6.25 1.20e+00 6.94e-01 2.71e+01 angle pdb=" CA TYR B 439 " pdb=" C TYR B 439 " pdb=" O TYR B 439 " ideal model delta sigma weight residual 120.90 115.83 5.07 1.07e+00 8.73e-01 2.25e+01 ... (remaining 23089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9300 17.86 - 35.72: 538 35.72 - 53.58: 57 53.58 - 71.44: 14 71.44 - 89.30: 6 Dihedral angle restraints: 9915 sinusoidal: 3759 harmonic: 6156 Sorted by residual: dihedral pdb=" C THR A 412 " pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual -122.00 -134.76 12.76 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C THR B 412 " pdb=" N THR B 412 " pdb=" CA THR B 412 " pdb=" CB THR B 412 " ideal model delta harmonic sigma weight residual -122.00 -134.31 12.31 0 2.50e+00 1.60e-01 2.42e+01 dihedral pdb=" C THR C 412 " pdb=" N THR C 412 " pdb=" CA THR C 412 " pdb=" CB THR C 412 " ideal model delta harmonic sigma weight residual -122.00 -134.23 12.23 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 9912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2142 0.083 - 0.166: 321 0.166 - 0.249: 23 0.249 - 0.332: 1 0.332 - 0.415: 3 Chirality restraints: 2490 Sorted by residual: chirality pdb=" CA THR A 412 " pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CB THR A 412 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA THR B 412 " pdb=" N THR B 412 " pdb=" C THR B 412 " pdb=" CB THR B 412 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA THR C 412 " pdb=" N THR C 412 " pdb=" C THR C 412 " pdb=" CB THR C 412 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 2487 not shown) Planarity restraints: 3039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 438 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C ASN B 438 " 0.089 2.00e-02 2.50e+03 pdb=" O ASN B 438 " -0.033 2.00e-02 2.50e+03 pdb=" N TYR B 439 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 414 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ARG B 414 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG B 414 " -0.021 2.00e-02 2.50e+03 pdb=" N TRP B 415 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 436 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN B 436 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN B 436 " -0.020 2.00e-02 2.50e+03 pdb=" N SER B 437 " -0.019 2.00e-02 2.50e+03 ... (remaining 3036 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 23 2.36 - 2.99: 8612 2.99 - 3.63: 23871 3.63 - 4.26: 42822 4.26 - 4.90: 70773 Nonbonded interactions: 146101 Sorted by model distance: nonbonded pdb=" OE1 GLU C 545 " pdb=" CE1 PHE C 594 " model vdw 1.725 3.340 nonbonded pdb=" OE1 GLU C 545 " pdb=" CZ PHE C 594 " model vdw 1.942 3.340 nonbonded pdb=" CB GLU C 545 " pdb=" CE1 PHE C 594 " model vdw 1.963 3.740 nonbonded pdb=" OD1 ASP A 589 " pdb=" NZ LYS B 587 " model vdw 2.094 2.520 nonbonded pdb=" O SER B 590 " pdb=" OG SER B 590 " model vdw 2.122 2.440 ... (remaining 146096 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 7.920 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 47.900 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.004 0.052 17007 Z= 0.287 Angle : 0.660 9.762 23094 Z= 0.452 Chirality : 0.055 0.415 2490 Planarity : 0.004 0.051 3039 Dihedral : 11.180 89.305 6009 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.17 % Allowed : 1.82 % Favored : 98.01 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.23 % 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: -3.14 (0.15), residues: 2142 helix: -3.67 (0.18), residues: 243 sheet: -1.16 (0.20), residues: 657 loop : -2.33 (0.14), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 782 HIS 0.003 0.001 HIS B 826 PHE 0.016 0.001 PHE B 413 TYR 0.013 0.001 TYR A 758 ARG 0.004 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: A 401 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7780 (ttt180) REVERT: A 612 GLU cc_start: 0.7990 (tt0) cc_final: 0.7601 (tt0) REVERT: A 874 MET cc_start: 0.8580 (mtm) cc_final: 0.8361 (mtp) REVERT: B 401 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7828 (ttt180) outliers start: 3 outliers final: 2 residues processed: 262 average time/residue: 1.3683 time to fit residues: 395.9154 Evaluate side-chains 141 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 741 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 0.0470 chunk 124 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 356 ASN A 367 ASN A 431 HIS A 438 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN A 501 GLN A 525 ASN A 533 GLN A 606 ASN A 671 HIS A 726 HIS A 902 ASN B 220 HIS B 306 GLN B 431 HIS B 438 ASN B 452 GLN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 525 ASN B 533 GLN B 548 ASN B 606 ASN B 671 HIS B 726 HIS B 853 GLN C 220 HIS C 306 GLN C 431 HIS C 438 ASN C 452 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN C 525 ASN C 606 ASN C 671 HIS C 687 ASN C 718 HIS C 726 HIS C 744 ASN C 893 ASN C 902 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17007 Z= 0.145 Angle : 0.491 6.338 23094 Z= 0.268 Chirality : 0.045 0.135 2490 Planarity : 0.004 0.060 3039 Dihedral : 4.677 25.676 2324 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.94 % Allowed : 8.02 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.52 (0.16), residues: 2142 helix: -2.06 (0.25), residues: 270 sheet: -0.92 (0.19), residues: 690 loop : -2.07 (0.15), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 782 HIS 0.003 0.001 HIS A 718 PHE 0.017 0.001 PHE C 382 TYR 0.009 0.001 TYR B 540 ARG 0.001 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8017 (tttp) REVERT: A 401 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7873 (ttt180) REVERT: A 612 GLU cc_start: 0.8002 (tt0) cc_final: 0.7577 (tt0) REVERT: A 874 MET cc_start: 0.8608 (mtm) cc_final: 0.8295 (mtp) REVERT: A 902 ASN cc_start: 0.8367 (m110) cc_final: 0.8094 (m-40) REVERT: B 572 ASP cc_start: 0.8253 (t70) cc_final: 0.8045 (t70) REVERT: B 602 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8744 (mm) REVERT: B 612 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7301 (mt-10) REVERT: B 684 THR cc_start: 0.8344 (t) cc_final: 0.8030 (m) REVERT: B 869 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6922 (p0) REVERT: C 545 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: C 572 ASP cc_start: 0.8290 (t0) cc_final: 0.8014 (t0) REVERT: C 597 LYS cc_start: 0.7613 (tmtt) cc_final: 0.7406 (tmtt) REVERT: C 612 GLU cc_start: 0.7807 (tt0) cc_final: 0.7604 (mt-10) REVERT: C 902 ASN cc_start: 0.8147 (m-40) cc_final: 0.7872 (m110) outliers start: 17 outliers final: 6 residues processed: 155 average time/residue: 1.2838 time to fit residues: 222.7416 Evaluate side-chains 143 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 869 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 0.0570 chunk 193 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 ASN B 436 GLN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN C 356 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 GLN C 718 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17007 Z= 0.285 Angle : 0.586 7.626 23094 Z= 0.321 Chirality : 0.049 0.161 2490 Planarity : 0.004 0.048 3039 Dihedral : 5.283 20.902 2323 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.55 % Allowed : 7.85 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.26 (0.16), residues: 2142 helix: -1.54 (0.28), residues: 270 sheet: -0.78 (0.20), residues: 693 loop : -1.97 (0.15), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 782 HIS 0.006 0.001 HIS C 431 PHE 0.022 0.002 PHE B 382 TYR 0.014 0.002 TYR B 540 ARG 0.003 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 401 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7873 (ttt180) REVERT: A 612 GLU cc_start: 0.8018 (tt0) cc_final: 0.7559 (tt0) REVERT: A 874 MET cc_start: 0.8678 (mtm) cc_final: 0.8460 (mtp) REVERT: A 902 ASN cc_start: 0.8379 (m110) cc_final: 0.8112 (m-40) REVERT: B 304 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.6711 (mmt) REVERT: B 395 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7573 (tmt170) REVERT: B 401 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7986 (ttt90) REVERT: B 545 GLU cc_start: 0.8043 (pt0) cc_final: 0.7737 (pt0) REVERT: B 602 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8861 (mm) REVERT: B 684 THR cc_start: 0.8358 (t) cc_final: 0.8079 (m) REVERT: C 612 GLU cc_start: 0.7792 (tt0) cc_final: 0.7577 (mt-10) REVERT: C 853 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7484 (mt0) outliers start: 28 outliers final: 9 residues processed: 161 average time/residue: 1.4540 time to fit residues: 258.3871 Evaluate side-chains 145 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 545 GLU Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.3980 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 184 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN B 902 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN C 902 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17007 Z= 0.173 Angle : 0.506 6.985 23094 Z= 0.276 Chirality : 0.046 0.139 2490 Planarity : 0.004 0.040 3039 Dihedral : 5.045 20.820 2323 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.22 % Allowed : 8.90 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.01 (0.17), residues: 2142 helix: -1.11 (0.31), residues: 270 sheet: -0.67 (0.20), residues: 693 loop : -1.83 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 782 HIS 0.003 0.001 HIS B 431 PHE 0.018 0.001 PHE B 382 TYR 0.008 0.001 TYR B 540 ARG 0.001 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.941 Fit side-chains REVERT: A 304 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7518 (mtp) REVERT: A 401 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7883 (ttt180) REVERT: A 587 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8292 (tttt) REVERT: A 612 GLU cc_start: 0.8008 (tt0) cc_final: 0.7548 (tt0) REVERT: B 304 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.6796 (mmt) REVERT: B 395 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7681 (tmt170) REVERT: B 401 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7983 (ttt90) REVERT: B 545 GLU cc_start: 0.8045 (pt0) cc_final: 0.7776 (pt0) REVERT: B 602 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8790 (mm) REVERT: B 684 THR cc_start: 0.8317 (t) cc_final: 0.8065 (m) REVERT: C 853 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7413 (mt0) outliers start: 22 outliers final: 4 residues processed: 158 average time/residue: 1.3959 time to fit residues: 244.3846 Evaluate side-chains 140 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN C 341 HIS ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17007 Z= 0.238 Angle : 0.552 7.481 23094 Z= 0.302 Chirality : 0.047 0.149 2490 Planarity : 0.004 0.038 3039 Dihedral : 5.235 20.902 2323 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.71 % Allowed : 8.79 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2142 helix: -0.99 (0.31), residues: 270 sheet: -0.64 (0.20), residues: 693 loop : -1.80 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 695 HIS 0.006 0.001 HIS B 431 PHE 0.021 0.002 PHE B 382 TYR 0.010 0.001 TYR B 540 ARG 0.002 0.000 ARG C 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 2.068 Fit side-chains REVERT: A 304 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7446 (mtp) REVERT: A 401 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7921 (ttt180) REVERT: A 587 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8381 (tttt) REVERT: A 602 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 612 GLU cc_start: 0.8005 (tt0) cc_final: 0.7534 (tt0) REVERT: A 902 ASN cc_start: 0.8310 (m110) cc_final: 0.8027 (m-40) REVERT: B 304 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.6767 (mmt) REVERT: B 395 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7675 (tmt170) REVERT: B 401 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7989 (ttt90) REVERT: B 545 GLU cc_start: 0.8035 (pt0) cc_final: 0.7828 (pt0) REVERT: B 602 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8821 (mm) REVERT: B 684 THR cc_start: 0.8307 (t) cc_final: 0.8073 (m) REVERT: C 782 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.7451 (m-10) REVERT: C 853 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7440 (mt0) outliers start: 31 outliers final: 10 residues processed: 154 average time/residue: 1.3771 time to fit residues: 235.3895 Evaluate side-chains 145 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 782 TRP Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 171 optimal weight: 0.0870 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN B 786 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17007 Z= 0.231 Angle : 0.545 7.807 23094 Z= 0.298 Chirality : 0.047 0.147 2490 Planarity : 0.004 0.038 3039 Dihedral : 5.250 21.558 2323 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.60 % Allowed : 9.01 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2142 helix: -0.89 (0.31), residues: 270 sheet: -0.63 (0.20), residues: 693 loop : -1.76 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 782 HIS 0.005 0.001 HIS B 431 PHE 0.021 0.001 PHE B 382 TYR 0.009 0.001 TYR B 540 ARG 0.002 0.000 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.961 Fit side-chains REVERT: A 195 ASP cc_start: 0.7258 (p0) cc_final: 0.7056 (p0) REVERT: A 304 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7450 (mtp) REVERT: A 401 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7937 (ttt180) REVERT: A 587 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8368 (tttt) REVERT: A 602 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8808 (mm) REVERT: A 612 GLU cc_start: 0.8006 (tt0) cc_final: 0.7537 (tt0) REVERT: A 873 GLN cc_start: 0.8282 (tt0) cc_final: 0.7854 (tt0) REVERT: B 304 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.6832 (mmt) REVERT: B 395 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7676 (tmt170) REVERT: B 401 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7985 (ttt90) REVERT: B 602 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8816 (mm) REVERT: C 853 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7426 (mt0) outliers start: 29 outliers final: 10 residues processed: 150 average time/residue: 1.3862 time to fit residues: 230.6415 Evaluate side-chains 143 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 741 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 117 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 116 optimal weight: 0.0980 chunk 173 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN B 392 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17007 Z= 0.171 Angle : 0.511 8.321 23094 Z= 0.279 Chirality : 0.046 0.138 2490 Planarity : 0.004 0.038 3039 Dihedral : 5.064 22.791 2323 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.33 % Allowed : 9.95 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2142 helix: -0.76 (0.32), residues: 270 sheet: -0.57 (0.20), residues: 693 loop : -1.67 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 782 HIS 0.004 0.001 HIS B 431 PHE 0.018 0.001 PHE B 382 TYR 0.009 0.001 TYR B 540 ARG 0.001 0.000 ARG C 799 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.860 Fit side-chains REVERT: A 195 ASP cc_start: 0.7257 (p0) cc_final: 0.7054 (p0) REVERT: A 304 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7395 (mtp) REVERT: A 401 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7922 (ttt180) REVERT: A 587 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8321 (tttt) REVERT: A 602 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8751 (mm) REVERT: A 612 GLU cc_start: 0.8009 (tt0) cc_final: 0.7532 (tt0) REVERT: A 873 GLN cc_start: 0.8305 (tt0) cc_final: 0.7886 (tt0) REVERT: B 395 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7665 (tmt170) REVERT: B 401 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7994 (ttt90) REVERT: B 602 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8790 (mm) REVERT: B 782 TRP cc_start: 0.7987 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: C 853 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7403 (mt0) outliers start: 24 outliers final: 11 residues processed: 148 average time/residue: 1.5083 time to fit residues: 246.8458 Evaluate side-chains 146 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 782 TRP Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain B residue 801 ASP Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 130 optimal weight: 0.2980 chunk 139 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 902 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17007 Z= 0.121 Angle : 0.478 7.824 23094 Z= 0.260 Chirality : 0.044 0.142 2490 Planarity : 0.003 0.040 3039 Dihedral : 4.826 21.632 2322 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.00 % Allowed : 10.34 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2142 helix: -0.65 (0.32), residues: 273 sheet: -0.55 (0.20), residues: 708 loop : -1.55 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 230 HIS 0.003 0.001 HIS C 431 PHE 0.015 0.001 PHE A 382 TYR 0.007 0.001 TYR C 819 ARG 0.002 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.942 Fit side-chains REVERT: A 304 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7378 (mtp) REVERT: A 401 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7907 (ttt180) REVERT: A 602 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 612 GLU cc_start: 0.7991 (tt0) cc_final: 0.7486 (tt0) REVERT: A 873 GLN cc_start: 0.8270 (tt0) cc_final: 0.7839 (tt0) REVERT: A 906 SER cc_start: 0.8280 (t) cc_final: 0.7921 (m) REVERT: B 395 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7740 (tmt170) REVERT: B 401 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7986 (ttt90) REVERT: B 602 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8756 (mm) REVERT: C 356 ASN cc_start: 0.7426 (m110) cc_final: 0.7175 (m-40) REVERT: C 853 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7400 (mt0) outliers start: 18 outliers final: 9 residues processed: 148 average time/residue: 1.3722 time to fit residues: 226.1170 Evaluate side-chains 146 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 115 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 172 optimal weight: 0.2980 chunk 180 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 ASN C 292 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17007 Z= 0.157 Angle : 0.497 7.565 23094 Z= 0.270 Chirality : 0.045 0.142 2490 Planarity : 0.004 0.039 3039 Dihedral : 4.873 20.971 2322 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.11 % Allowed : 10.34 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2142 helix: -0.58 (0.32), residues: 270 sheet: -0.53 (0.20), residues: 708 loop : -1.53 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 782 HIS 0.003 0.001 HIS B 431 PHE 0.017 0.001 PHE B 382 TYR 0.008 0.001 TYR C 540 ARG 0.001 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.918 Fit side-chains REVERT: A 304 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7388 (mtp) REVERT: A 401 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7867 (ttt180) REVERT: A 602 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8765 (mm) REVERT: A 612 GLU cc_start: 0.7987 (tt0) cc_final: 0.7480 (tt0) REVERT: A 873 GLN cc_start: 0.8288 (tt0) cc_final: 0.7837 (tt0) REVERT: A 902 ASN cc_start: 0.8287 (m110) cc_final: 0.8085 (m-40) REVERT: A 906 SER cc_start: 0.8277 (t) cc_final: 0.7901 (m) REVERT: B 304 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7129 (mtp) REVERT: B 395 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7764 (tmt170) REVERT: B 401 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7983 (ttt90) REVERT: B 602 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8773 (mm) REVERT: C 853 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7409 (mt0) outliers start: 20 outliers final: 9 residues processed: 143 average time/residue: 1.3459 time to fit residues: 214.0953 Evaluate side-chains 143 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 195 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN C 356 ASN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17007 Z= 0.164 Angle : 0.501 7.830 23094 Z= 0.272 Chirality : 0.045 0.141 2490 Planarity : 0.004 0.039 3039 Dihedral : 4.915 21.319 2322 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.00 % Allowed : 10.61 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2142 helix: -0.60 (0.32), residues: 270 sheet: -0.53 (0.20), residues: 708 loop : -1.52 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 782 HIS 0.004 0.001 HIS B 431 PHE 0.018 0.001 PHE B 382 TYR 0.009 0.001 TYR A 454 ARG 0.001 0.000 ARG C 799 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.951 Fit side-chains REVERT: A 304 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7414 (mtp) REVERT: A 401 ARG cc_start: 0.8131 (ttm-80) cc_final: 0.7882 (ttt180) REVERT: A 587 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8271 (tttt) REVERT: A 602 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 612 GLU cc_start: 0.7987 (tt0) cc_final: 0.7508 (tt0) REVERT: A 873 GLN cc_start: 0.8283 (tt0) cc_final: 0.7902 (tt0) REVERT: B 304 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7195 (mtp) REVERT: B 395 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7773 (tmt170) REVERT: B 401 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7981 (ttt90) REVERT: B 602 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8772 (mm) REVERT: C 356 ASN cc_start: 0.7460 (m-40) cc_final: 0.7230 (m-40) REVERT: C 853 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7417 (mt0) outliers start: 18 outliers final: 10 residues processed: 140 average time/residue: 1.4618 time to fit residues: 225.9623 Evaluate side-chains 144 residues out of total 1809 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 853 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN C 452 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.086764 restraints weight = 18309.895| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.33 r_work: 0.2778 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17007 Z= 0.300 Angle : 0.587 8.034 23094 Z= 0.321 Chirality : 0.049 0.162 2490 Planarity : 0.004 0.038 3039 Dihedral : 5.366 23.361 2322 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.88 % Allowed : 10.78 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2142 helix: -0.75 (0.32), residues: 270 sheet: -0.58 (0.20), residues: 708 loop : -1.64 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 782 HIS 0.006 0.001 HIS B 431 PHE 0.022 0.002 PHE A 382 TYR 0.015 0.002 TYR A 454 ARG 0.002 0.000 ARG C 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5072.03 seconds wall clock time: 91 minutes 7.84 seconds (5467.84 seconds total)