Starting phenix.real_space_refine (version: dev) on Tue Apr 5 21:17:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/04_2022/7l2k_23131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/04_2022/7l2k_23131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/04_2022/7l2k_23131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/04_2022/7l2k_23131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/04_2022/7l2k_23131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2k_23131/04_2022/7l2k_23131.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 212": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 15998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 480, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 480, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3998 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 480, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 4000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4000 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 480, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.07, per 1000 atoms: 0.57 Number of scatterers: 15998 At special positions: 0 Unit cell: (127.65, 127.65, 111.55, 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 100 16.00 O 2816 8.00 N 2588 7.00 C 10494 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: 6.63 Conformation dependent library (CDL) restraints added in 2.3 seconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 4 sheets defined 68.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.738A pdb=" N VAL A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.616A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.919A pdb=" N VAL A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.767A pdb=" N ALA A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.848A pdb=" N SER A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.005A pdb=" N LEU A 365 " --> pdb=" O CYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.797A pdb=" N ASN A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.537A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 498 removed outlier: 3.600A pdb=" N TYR A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 510 through 532 removed outlier: 4.262A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.708A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.666A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 599 removed outlier: 4.919A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 640 removed outlier: 3.941A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 655 through 671 Processing helix chain 'A' and resid 673 through 689 removed outlier: 3.512A pdb=" N ASN A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 712 removed outlier: 3.662A pdb=" N SER A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 216 through 221 removed outlier: 4.003A pdb=" N VAL C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.881A pdb=" N THR C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.647A pdb=" N ALA C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 320 removed outlier: 3.780A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 362 through 366 removed outlier: 4.138A pdb=" N LEU C 365 " --> pdb=" O CYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.534A pdb=" N ASN C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 498 removed outlier: 3.650A pdb=" N TYR C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.592A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 removed outlier: 3.563A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 599 removed outlier: 3.947A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 Processing helix chain 'C' and resid 640 through 643 Processing helix chain 'C' and resid 655 through 671 Processing helix chain 'C' and resid 673 through 712 removed outlier: 3.759A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 Processing helix chain 'D' and resid 216 through 221 removed outlier: 3.662A pdb=" N VAL D 221 " --> pdb=" O VAL D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.654A pdb=" N THR D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 268 removed outlier: 3.990A pdb=" N LEU D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.505A pdb=" N ALA D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 320 removed outlier: 3.811A pdb=" N SER D 307 " --> pdb=" O LYS D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 346 through 354 Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.968A pdb=" N LEU D 365 " --> pdb=" O CYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.740A pdb=" N ASN D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 498 removed outlier: 3.623A pdb=" N TYR D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.617A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 removed outlier: 3.697A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 599 removed outlier: 4.874A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 640 removed outlier: 3.942A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 643 No H-bonds generated for 'chain 'D' and resid 641 through 643' Processing helix chain 'D' and resid 655 through 671 Processing helix chain 'D' and resid 673 through 689 Processing helix chain 'D' and resid 691 through 712 removed outlier: 3.533A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.740A pdb=" N VAL B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.759A pdb=" N THR B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 267 removed outlier: 3.896A pdb=" N VAL B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.504A pdb=" N ALA B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.880A pdb=" N SER B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 362 through 366 removed outlier: 4.032A pdb=" N LEU B 365 " --> pdb=" O CYS B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.787A pdb=" N ASN B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 498 removed outlier: 3.610A pdb=" N TYR B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.749A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.622A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 removed outlier: 3.660A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 599 removed outlier: 4.972A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 640 removed outlier: 3.960A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 643 No H-bonds generated for 'chain 'B' and resid 641 through 643' Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 673 through 712 removed outlier: 6.053A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.728A pdb=" N SER A 379 " --> pdb=" O TRP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 368 through 373 removed outlier: 5.369A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.516A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 368 through 373 removed outlier: 4.086A pdb=" N GLU B 371 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2712 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: 4.56 Time building geometry restraints manager: 7.10 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: 4854 1.34 - 1.46: 3547 1.46 - 1.58: 7797 1.58 - 1.70: 0 1.70 - 1.81: 164 Bond restraints: 16362 Sorted by residual: bond pdb=" C ASN B 652 " pdb=" N TYR B 653 " ideal model delta sigma weight residual 1.332 1.221 0.111 1.40e-02 5.10e+03 6.28e+01 bond pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 1.332 1.258 0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" CA TYR C 555 " pdb=" C TYR C 555 " ideal model delta sigma weight residual 1.523 1.468 0.054 1.41e-02 5.03e+03 1.49e+01 bond pdb=" C THR C 650 " pdb=" N GLU C 651 " ideal model delta sigma weight residual 1.332 1.368 -0.035 1.29e-02 6.01e+03 7.41e+00 bond pdb=" C ASN D 652 " pdb=" N TYR D 653 " ideal model delta sigma weight residual 1.332 1.295 0.037 1.40e-02 5.10e+03 6.99e+00 ... (remaining 16357 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.14: 198 104.14 - 111.63: 7432 111.63 - 119.13: 5923 119.13 - 126.62: 8423 126.62 - 134.12: 177 Bond angle restraints: 22153 Sorted by residual: angle pdb=" CA ASN C 652 " pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 116.43 108.51 7.92 1.37e+00 5.33e-01 3.34e+01 angle pdb=" O ASN C 652 " pdb=" C ASN C 652 " pdb=" N TYR C 653 " ideal model delta sigma weight residual 122.96 129.66 -6.70 1.26e+00 6.30e-01 2.83e+01 angle pdb=" C THR B 650 " pdb=" N GLU B 651 " pdb=" CA GLU B 651 " ideal model delta sigma weight residual 122.60 116.94 5.66 1.56e+00 4.11e-01 1.32e+01 angle pdb=" C PHE B 712 " pdb=" N LEU B 713 " pdb=" CA LEU B 713 " ideal model delta sigma weight residual 121.54 128.43 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" C ASN D 652 " pdb=" N TYR D 653 " pdb=" CA TYR D 653 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 ... (remaining 22148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 8899 15.71 - 31.41: 657 31.41 - 47.12: 89 47.12 - 62.83: 24 62.83 - 78.54: 10 Dihedral angle restraints: 9679 sinusoidal: 3839 harmonic: 5840 Sorted by residual: dihedral pdb=" CA PRO A 732 " pdb=" C PRO A 732 " pdb=" N ASP A 733 " pdb=" CA ASP A 733 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA SER A 711 " pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR D 389 " pdb=" C THR D 389 " pdb=" N CYS D 390 " pdb=" CA CYS D 390 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1487 0.035 - 0.069: 773 0.069 - 0.104: 224 0.104 - 0.138: 54 0.138 - 0.173: 9 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CG LEU C 637 " pdb=" CB LEU C 637 " pdb=" CD1 LEU C 637 " pdb=" CD2 LEU C 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE B 689 " pdb=" CA ILE B 689 " pdb=" CG1 ILE B 689 " pdb=" CG2 ILE B 689 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CG LEU A 637 " pdb=" CB LEU A 637 " pdb=" CD1 LEU A 637 " pdb=" CD2 LEU A 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.93e-01 ... (remaining 2544 not shown) Planarity restraints: 2724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 650 " -0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C THR C 650 " 0.068 2.00e-02 2.50e+03 pdb=" O THR C 650 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU C 651 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 650 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C THR B 650 " -0.064 2.00e-02 2.50e+03 pdb=" O THR B 650 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU B 651 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 548 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C GLY C 548 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY C 548 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP C 549 " -0.015 2.00e-02 2.50e+03 ... (remaining 2721 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 114 2.59 - 3.16: 14465 3.16 - 3.74: 24044 3.74 - 4.32: 32807 4.32 - 4.90: 54071 Nonbonded interactions: 125501 Sorted by model distance: nonbonded pdb=" OG1 THR A 731 " pdb=" O ASP A 733 " model vdw 2.007 2.440 nonbonded pdb=" OG1 THR C 731 " pdb=" O ASP C 733 " model vdw 2.026 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" O ASP D 733 " model vdw 2.029 2.440 nonbonded pdb=" OE1 GLU C 651 " pdb=" NZ LYS C 656 " model vdw 2.073 2.520 nonbonded pdb=" O ILE D 672 " pdb=" ND2 ASN D 676 " model vdw 2.108 2.520 ... (remaining 125496 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = (chain 'B' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = (chain 'C' and (resid 203 through 727 or (resid 728 and (name N or name CA or na \ me C or name O or name CB )) or resid 729 through 745)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10494 2.51 5 N 2588 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.130 Process input model: 41.880 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.008 0.111 16362 Z= 0.504 Angle : 0.819 7.921 22153 Z= 0.466 Chirality : 0.044 0.173 2547 Planarity : 0.005 0.040 2724 Dihedral : 11.267 78.535 5911 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.56 % Favored : 93.24 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.05 (0.19), residues: 1952 helix: 1.07 (0.14), residues: 1196 sheet: 0.16 (0.76), residues: 36 loop : -1.97 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 772 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 778 average time/residue: 0.2635 time to fit residues: 300.3067 Evaluate side-chains 486 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 483 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1341 time to fit residues: 3.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 8.9990 chunk 148 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 0.0770 chunk 177 optimal weight: 8.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 519 GLN A 560 GLN A 561 GLN D 354 GLN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN D 652 ASN D 727 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN B 560 GLN B 561 GLN B 727 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 16362 Z= 0.208 Angle : 0.687 11.375 22153 Z= 0.355 Chirality : 0.040 0.159 2547 Planarity : 0.004 0.050 2724 Dihedral : 4.716 17.518 2172 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.50 (0.19), residues: 1952 helix: 1.61 (0.14), residues: 1196 sheet: 0.43 (0.76), residues: 36 loop : -1.96 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 644 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 38 residues processed: 662 average time/residue: 0.2616 time to fit residues: 258.1518 Evaluate side-chains 537 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 499 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2063 time to fit residues: 15.6943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN C 519 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 16362 Z= 0.278 Angle : 0.713 13.745 22153 Z= 0.359 Chirality : 0.041 0.202 2547 Planarity : 0.005 0.072 2724 Dihedral : 4.718 20.860 2172 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.28 (0.19), residues: 1952 helix: 1.44 (0.15), residues: 1204 sheet: -0.07 (0.71), residues: 36 loop : -2.09 (0.22), residues: 712 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 518 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 34 residues processed: 543 average time/residue: 0.2701 time to fit residues: 223.5795 Evaluate side-chains 512 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 478 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1641 time to fit residues: 12.7829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 560 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16362 Z= 0.192 Angle : 0.703 13.216 22153 Z= 0.353 Chirality : 0.040 0.302 2547 Planarity : 0.004 0.079 2724 Dihedral : 4.616 21.446 2172 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.19), residues: 1952 helix: 1.47 (0.15), residues: 1208 sheet: 0.44 (0.77), residues: 36 loop : -2.14 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 537 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 545 average time/residue: 0.2504 time to fit residues: 205.5757 Evaluate side-chains 496 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 481 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1762 time to fit residues: 7.2123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.9990 chunk 107 optimal weight: 0.0570 chunk 2 optimal weight: 0.2980 chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 561 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 16362 Z= 0.188 Angle : 0.736 19.026 22153 Z= 0.365 Chirality : 0.041 0.349 2547 Planarity : 0.004 0.055 2724 Dihedral : 4.531 20.499 2172 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.30 (0.19), residues: 1952 helix: 1.44 (0.15), residues: 1208 sheet: 0.59 (0.80), residues: 36 loop : -2.11 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 551 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 560 average time/residue: 0.2540 time to fit residues: 213.2860 Evaluate side-chains 504 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 495 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1398 time to fit residues: 5.0226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 0.2980 chunk 37 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 0.0170 chunk 87 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.156 16362 Z= 0.224 Angle : 0.773 16.223 22153 Z= 0.387 Chirality : 0.041 0.293 2547 Planarity : 0.004 0.045 2724 Dihedral : 4.502 18.976 2172 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.23 (0.19), residues: 1952 helix: 1.41 (0.15), residues: 1208 sheet: -0.07 (0.74), residues: 36 loop : -2.16 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 516 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 529 average time/residue: 0.2638 time to fit residues: 208.6588 Evaluate side-chains 519 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 500 time to evaluate : 1.746 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1903 time to fit residues: 8.5239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.0370 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 159 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.602 16362 Z= 0.374 Angle : 1.004 73.891 22153 Z= 0.469 Chirality : 0.044 0.440 2547 Planarity : 0.004 0.053 2724 Dihedral : 4.498 18.934 2172 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.21 (0.19), residues: 1952 helix: 1.40 (0.15), residues: 1208 sheet: -0.13 (0.75), residues: 36 loop : -2.19 (0.22), residues: 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 502 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 508 average time/residue: 0.2666 time to fit residues: 201.5913 Evaluate side-chains 488 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 482 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1445 time to fit residues: 4.3770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 148 optimal weight: 0.0040 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.574 16362 Z= 0.409 Angle : 1.031 73.888 22153 Z= 0.499 Chirality : 0.045 0.499 2547 Planarity : 0.004 0.053 2724 Dihedral : 4.515 18.911 2172 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 7.69 % 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: 0.19 (0.19), residues: 1952 helix: 1.39 (0.15), residues: 1208 sheet: -0.14 (0.75), residues: 36 loop : -2.19 (0.21), residues: 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 489 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 493 average time/residue: 0.2625 time to fit residues: 193.8419 Evaluate side-chains 491 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 480 time to evaluate : 1.931 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1477 time to fit residues: 5.8496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 0.0060 chunk 176 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.452 16362 Z= 1.085 Angle : 1.219 92.099 22153 Z= 0.652 Chirality : 0.045 0.499 2547 Planarity : 0.004 0.053 2724 Dihedral : 4.515 18.911 2172 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 7.69 % 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: 0.19 (0.19), residues: 1952 helix: 1.39 (0.15), residues: 1208 sheet: -0.14 (0.75), residues: 36 loop : -2.19 (0.21), residues: 708 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.2627 time to fit residues: 194.9644 Evaluate side-chains 478 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 1.810 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 88 optimal weight: 0.0980 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.452 16362 Z= 1.085 Angle : 1.219 92.099 22153 Z= 0.652 Chirality : 0.045 0.499 2547 Planarity : 0.004 0.053 2724 Dihedral : 4.515 18.911 2172 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 7.69 % 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: 0.19 (0.19), residues: 1952 helix: 1.39 (0.15), residues: 1208 sheet: -0.14 (0.75), residues: 36 loop : -2.19 (0.21), residues: 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 0.2638 time to fit residues: 189.4583 Evaluate side-chains 480 residues out of total 1768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 0.0370 chunk 47 optimal weight: 30.0000 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 GLN ** D 676 ASN ** 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 = 0.4316 r_free = 0.4316 target = 0.192271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.142038 restraints weight = 29240.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145854 restraints weight = 15057.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148196 restraints weight = 9875.429| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 1.452 16362 Z= 1.085 Angle : 1.219 92.099 22153 Z= 0.652 Chirality : 0.045 0.499 2547 Planarity : 0.004 0.053 2724 Dihedral : 4.515 18.911 2172 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 7.69 % 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: 0.19 (0.19), residues: 1952 helix: 1.39 (0.15), residues: 1208 sheet: -0.14 (0.75), residues: 36 loop : -2.19 (0.21), residues: 708 =============================================================================== Job complete usr+sys time: 3937.94 seconds wall clock time: 71 minutes 57.05 seconds (4317.05 seconds total)