Starting phenix.real_space_refine on Fri Mar 15 21:04:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/03_2024/8a9a_15274.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/03_2024/8a9a_15274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/03_2024/8a9a_15274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/03_2024/8a9a_15274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/03_2024/8a9a_15274.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/03_2024/8a9a_15274.pdb" } resolution = 3.3 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= 0.033 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 16 5.16 5 C 8240 2.51 5 N 2054 2.21 5 O 2462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 102": "OD1" <-> "OD2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 496": "OE1" <-> "OE2" Residue "B ASP 559": "OD1" <-> "OD2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 771": "OD1" <-> "OD2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 771": "OD1" <-> "OD2" Residue "A PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12772 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6386 Classifications: {'peptide': 809} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 786} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 6386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6386 Classifications: {'peptide': 809} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 786} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 6.65, per 1000 atoms: 0.52 Number of scatterers: 12772 At special positions: 0 Unit cell: (86.1, 115.5, 257.25, 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 16 16.00 O 2462 8.00 N 2054 7.00 C 8240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.0 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 6 sheets defined 46.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'B' and resid 95 through 106 removed outlier: 4.063A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 125 removed outlier: 3.766A pdb=" N ALA B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.171A pdb=" N ASN B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 267 Processing helix chain 'B' and resid 268 through 294 removed outlier: 3.554A pdb=" N ILE B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.649A pdb=" N GLU B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 removed outlier: 4.023A pdb=" N LYS B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 removed outlier: 3.708A pdb=" N ARG B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 removed outlier: 3.663A pdb=" N LYS B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.598A pdb=" N ASP B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.866A pdb=" N SER B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 393 through 415 removed outlier: 4.583A pdb=" N ASP B 406 " --> pdb=" O GLN B 402 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Proline residue: B 410 - end of helix Processing helix chain 'B' and resid 421 through 429 removed outlier: 3.690A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 443 through 462 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.882A pdb=" N LEU B 484 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 486 " --> pdb=" O ASP B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 499 removed outlier: 4.189A pdb=" N ALA B 495 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.976A pdb=" N ASP B 514 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 525 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.108A pdb=" N GLU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 557' Processing helix chain 'B' and resid 565 through 584 removed outlier: 4.136A pdb=" N GLU B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 593 removed outlier: 4.018A pdb=" N LYS B 593 " --> pdb=" O THR B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.584A pdb=" N LEU B 644 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 Processing helix chain 'B' and resid 663 through 674 Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.819A pdb=" N PHE B 697 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 716 Processing helix chain 'B' and resid 719 through 723 Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'A' and resid 95 through 106 removed outlier: 4.062A pdb=" N GLY A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 125 removed outlier: 3.767A pdb=" N ALA A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.171A pdb=" N ASN A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 268 through 294 removed outlier: 3.554A pdb=" N ILE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.649A pdb=" N GLU A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 removed outlier: 4.023A pdb=" N LYS A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.708A pdb=" N ARG A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.663A pdb=" N LYS A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.598A pdb=" N ASP A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.867A pdb=" N SER A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 393 through 415 removed outlier: 4.584A pdb=" N ASP A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Proline residue: A 410 - end of helix Processing helix chain 'A' and resid 421 through 429 removed outlier: 3.690A pdb=" N ILE A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 443 through 462 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 486 removed outlier: 3.882A pdb=" N LEU A 484 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 removed outlier: 4.189A pdb=" N ALA A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.977A pdb=" N ASP A 514 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 525 Processing helix chain 'A' and resid 532 through 540 Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.110A pdb=" N GLU A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'A' and resid 565 through 584 removed outlier: 4.137A pdb=" N GLU A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.017A pdb=" N LYS A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.583A pdb=" N LEU A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.818A pdb=" N PHE A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 716 Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 797 through 816 Processing sheet with id=AA1, first strand: chain 'B' and resid 135 through 143 removed outlier: 5.485A pdb=" N LEU B 136 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR B 160 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG B 158 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 140 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA B 151 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA B 193 " --> pdb=" O ALA B 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 184 through 194 current: chain 'B' and resid 211 through 219 removed outlier: 7.590A pdb=" N MET B 213 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER B 228 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 215 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 217 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.551A pdb=" N VAL B 179 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 595 through 598 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 595 through 598 current: chain 'B' and resid 615 through 620 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 615 through 620 current: chain 'B' and resid 728 through 750 removed outlier: 9.593A pdb=" N TYR B 740 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N ILE B 770 " --> pdb=" O TYR B 740 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N GLY B 742 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N THR B 768 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASN B 744 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N VAL B 766 " --> pdb=" O ASN B 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 746 " --> pdb=" O ILE B 764 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 143 removed outlier: 5.485A pdb=" N LEU A 136 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 160 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ARG A 158 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 140 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 151 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA A 193 " --> pdb=" O ALA A 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 194 current: chain 'A' and resid 211 through 219 removed outlier: 7.589A pdb=" N MET A 213 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N SER A 228 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP A 215 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 217 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.552A pdb=" N VAL A 179 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 598 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 595 through 598 current: chain 'A' and resid 615 through 620 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 615 through 620 current: chain 'A' and resid 728 through 750 removed outlier: 9.594A pdb=" N TYR A 740 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N ILE A 770 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLY A 742 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N THR A 768 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N ASN A 744 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N VAL A 766 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 746 " --> pdb=" O ILE A 764 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1332 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: 3.83 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4078 1.34 - 1.46: 2682 1.46 - 1.58: 6202 1.58 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 12994 Sorted by residual: bond pdb=" CB LYS A 363 " pdb=" CG LYS A 363 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB LYS B 363 " pdb=" CG LYS B 363 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" N PRO B 61 " pdb=" CA PRO B 61 " ideal model delta sigma weight residual 1.469 1.454 0.014 1.28e-02 6.10e+03 1.26e+00 bond pdb=" N PRO A 61 " pdb=" CA PRO A 61 " ideal model delta sigma weight residual 1.469 1.455 0.014 1.28e-02 6.10e+03 1.23e+00 bond pdb=" CB ASN B 328 " pdb=" CG ASN B 328 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.11e-01 ... (remaining 12989 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.26: 243 107.26 - 113.94: 7404 113.94 - 120.62: 5193 120.62 - 127.30: 4617 127.30 - 133.98: 55 Bond angle restraints: 17512 Sorted by residual: angle pdb=" N PRO A 61 " pdb=" CA PRO A 61 " pdb=" CB PRO A 61 " ideal model delta sigma weight residual 103.25 110.58 -7.33 1.05e+00 9.07e-01 4.88e+01 angle pdb=" N PRO B 61 " pdb=" CA PRO B 61 " pdb=" CB PRO B 61 " ideal model delta sigma weight residual 103.25 110.55 -7.30 1.05e+00 9.07e-01 4.83e+01 angle pdb=" N LEU B 546 " pdb=" CA LEU B 546 " pdb=" C LEU B 546 " ideal model delta sigma weight residual 114.31 109.99 4.32 1.29e+00 6.01e-01 1.12e+01 angle pdb=" N LEU A 546 " pdb=" CA LEU A 546 " pdb=" C LEU A 546 " ideal model delta sigma weight residual 114.31 110.03 4.28 1.29e+00 6.01e-01 1.10e+01 angle pdb=" CA LYS B 363 " pdb=" CB LYS B 363 " pdb=" CG LYS B 363 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 17507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6597 17.65 - 35.29: 991 35.29 - 52.94: 244 52.94 - 70.59: 46 70.59 - 88.24: 20 Dihedral angle restraints: 7898 sinusoidal: 3178 harmonic: 4720 Sorted by residual: dihedral pdb=" CA PHE B 817 " pdb=" C PHE B 817 " pdb=" N GLN B 818 " pdb=" CA GLN B 818 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE A 817 " pdb=" C PHE A 817 " pdb=" N GLN A 818 " pdb=" CA GLN A 818 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU B 524 " pdb=" C LEU B 524 " pdb=" N LEU B 525 " pdb=" CA LEU B 525 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 7895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1509 0.044 - 0.088: 378 0.088 - 0.132: 94 0.132 - 0.176: 11 0.176 - 0.219: 6 Chirality restraints: 1998 Sorted by residual: chirality pdb=" CA PRO B 61 " pdb=" N PRO B 61 " pdb=" C PRO B 61 " pdb=" CB PRO B 61 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PRO A 61 " pdb=" N PRO A 61 " pdb=" C PRO A 61 " pdb=" CB PRO A 61 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PHE B 111 " pdb=" N PHE B 111 " pdb=" C PHE B 111 " pdb=" CB PHE B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1995 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 331 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO B 332 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 332 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 332 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 331 " 0.059 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A 332 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 374 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 375 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.045 5.00e-02 4.00e+02 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 265 2.67 - 3.23: 12490 3.23 - 3.79: 19940 3.79 - 4.34: 27205 4.34 - 4.90: 44018 Nonbonded interactions: 103918 Sorted by model distance: nonbonded pdb=" OG1 THR B 144 " pdb=" OG SER B 152 " model vdw 2.116 2.440 nonbonded pdb=" OG1 THR A 144 " pdb=" OG SER A 152 " model vdw 2.117 2.440 nonbonded pdb=" O THR A 610 " pdb=" OG1 THR A 613 " model vdw 2.201 2.440 nonbonded pdb=" O THR B 610 " pdb=" OG1 THR B 613 " model vdw 2.202 2.440 nonbonded pdb=" O ILE B 816 " pdb=" OH TYR B 821 " model vdw 2.233 2.440 ... (remaining 103913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.830 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 34.510 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12994 Z= 0.190 Angle : 0.666 8.999 17512 Z= 0.345 Chirality : 0.043 0.219 1998 Planarity : 0.005 0.090 2242 Dihedral : 18.003 88.236 4838 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.53 % Favored : 89.10 % Rotamer: Outliers : 0.14 % Allowed : 29.36 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.21), residues: 1614 helix: 0.19 (0.21), residues: 640 sheet: -0.07 (0.46), residues: 136 loop : -2.12 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 681 HIS 0.005 0.001 HIS B 580 PHE 0.016 0.001 PHE B 485 TYR 0.010 0.001 TYR A 761 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 284 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 LEU cc_start: 0.8492 (mt) cc_final: 0.8268 (mt) REVERT: B 465 MET cc_start: 0.5288 (mmp) cc_final: 0.5043 (mmm) REVERT: B 711 PHE cc_start: 0.7701 (m-80) cc_final: 0.7487 (m-80) REVERT: A 534 ASP cc_start: 0.4215 (t70) cc_final: 0.3934 (t0) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.2740 time to fit residues: 109.3255 Evaluate side-chains 148 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 781 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 30.0000 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN B 279 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 746 ASN A 584 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN A 803 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12994 Z= 0.384 Angle : 0.767 9.199 17512 Z= 0.395 Chirality : 0.048 0.224 1998 Planarity : 0.005 0.075 2242 Dihedral : 5.427 33.906 1682 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.28 % Favored : 88.35 % Rotamer: Outliers : 5.86 % Allowed : 26.14 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.92 (0.20), residues: 1614 helix: -0.52 (0.20), residues: 664 sheet: -0.70 (0.44), residues: 148 loop : -2.06 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 681 HIS 0.007 0.002 HIS B 580 PHE 0.019 0.002 PHE A 690 TYR 0.024 0.002 TYR A 623 ARG 0.005 0.001 ARG A 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 148 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.6449 (ppp) cc_final: 0.6103 (ppp) REVERT: B 695 ASN cc_start: 0.7534 (t0) cc_final: 0.7149 (t0) REVERT: A 393 ASP cc_start: 0.4284 (OUTLIER) cc_final: 0.3606 (t70) REVERT: A 500 THR cc_start: 0.7435 (m) cc_final: 0.6745 (p) REVERT: A 543 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.6226 (p0) REVERT: A 714 MET cc_start: 0.8368 (ttt) cc_final: 0.8141 (ttt) outliers start: 82 outliers final: 32 residues processed: 222 average time/residue: 0.2149 time to fit residues: 72.0298 Evaluate side-chains 143 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 746 ASN Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 0.0570 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 0.0010 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 459 GLN B 746 ASN A 235 ASN A 245 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12994 Z= 0.223 Angle : 0.640 8.009 17512 Z= 0.327 Chirality : 0.044 0.229 1998 Planarity : 0.004 0.058 2242 Dihedral : 5.042 25.458 1680 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.04 % Favored : 89.59 % Rotamer: Outliers : 5.43 % Allowed : 27.00 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.91 (0.20), residues: 1614 helix: -0.46 (0.20), residues: 660 sheet: -0.56 (0.45), residues: 144 loop : -2.12 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 681 HIS 0.007 0.002 HIS A 580 PHE 0.016 0.001 PHE B 232 TYR 0.019 0.001 TYR B 79 ARG 0.006 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 127 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 LEU cc_start: 0.8494 (mt) cc_final: 0.8291 (mt) REVERT: B 341 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7737 (tt) REVERT: B 695 ASN cc_start: 0.7332 (t0) cc_final: 0.7029 (t0) REVERT: B 864 LEU cc_start: 0.4840 (tp) cc_final: 0.4580 (tp) REVERT: A 347 GLN cc_start: 0.6468 (tp-100) cc_final: 0.5452 (mp10) REVERT: A 393 ASP cc_start: 0.4495 (OUTLIER) cc_final: 0.4193 (t70) REVERT: A 668 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7080 (tttt) REVERT: A 695 ASN cc_start: 0.6082 (t0) cc_final: 0.5820 (t0) outliers start: 76 outliers final: 35 residues processed: 196 average time/residue: 0.2096 time to fit residues: 63.4432 Evaluate side-chains 146 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 0.0370 chunk 41 optimal weight: 0.4980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12994 Z= 0.299 Angle : 0.696 8.425 17512 Z= 0.355 Chirality : 0.045 0.170 1998 Planarity : 0.004 0.048 2242 Dihedral : 5.267 26.256 1680 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.46 % Favored : 88.17 % Rotamer: Outliers : 5.79 % Allowed : 26.14 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.16 (0.20), residues: 1614 helix: -0.72 (0.19), residues: 652 sheet: -1.03 (0.43), residues: 160 loop : -2.14 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.007 0.002 HIS B 580 PHE 0.020 0.002 PHE A 327 TYR 0.015 0.002 TYR A 623 ARG 0.005 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 120 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7739 (tt) REVERT: B 453 ASN cc_start: 0.7373 (p0) cc_final: 0.7132 (p0) REVERT: B 454 PHE cc_start: 0.7054 (t80) cc_final: 0.6805 (t80) REVERT: B 637 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7147 (tt) REVERT: B 695 ASN cc_start: 0.7387 (t0) cc_final: 0.7095 (t0) REVERT: A 347 GLN cc_start: 0.6668 (tp-100) cc_final: 0.5475 (mp10) REVERT: A 364 THR cc_start: 0.5258 (OUTLIER) cc_final: 0.4867 (m) REVERT: A 496 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8055 (tt0) REVERT: A 543 ASN cc_start: 0.7567 (OUTLIER) cc_final: 0.6753 (p0) REVERT: A 668 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7155 (tttt) REVERT: A 695 ASN cc_start: 0.6581 (t0) cc_final: 0.6257 (t0) REVERT: A 835 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7319 (p0) outliers start: 81 outliers final: 45 residues processed: 193 average time/residue: 0.2045 time to fit residues: 61.1141 Evaluate side-chains 153 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 102 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 828 GLN Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 0.0170 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.0980 chunk 106 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 367 ASN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12994 Z= 0.228 Angle : 0.657 13.338 17512 Z= 0.330 Chirality : 0.043 0.165 1998 Planarity : 0.004 0.045 2242 Dihedral : 5.128 27.412 1680 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.10 % Favored : 89.65 % Rotamer: Outliers : 5.86 % Allowed : 27.14 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1614 helix: -0.61 (0.19), residues: 646 sheet: -0.92 (0.44), residues: 160 loop : -2.03 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 121 HIS 0.006 0.002 HIS B 580 PHE 0.019 0.001 PHE B 111 TYR 0.013 0.001 TYR B 79 ARG 0.008 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 119 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7644 (tt) REVERT: B 458 PHE cc_start: 0.7221 (t80) cc_final: 0.6949 (t80) REVERT: B 695 ASN cc_start: 0.7323 (t0) cc_final: 0.7047 (t0) REVERT: A 347 GLN cc_start: 0.6535 (tp-100) cc_final: 0.5264 (mp10) REVERT: A 496 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8135 (tt0) REVERT: A 543 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6649 (p0) REVERT: A 668 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.7180 (tttt) REVERT: A 695 ASN cc_start: 0.6700 (t0) cc_final: 0.6411 (t0) REVERT: A 746 ASN cc_start: 0.7334 (p0) cc_final: 0.7027 (p0) REVERT: A 835 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7395 (p0) outliers start: 82 outliers final: 50 residues processed: 193 average time/residue: 0.2049 time to fit residues: 61.7887 Evaluate side-chains 158 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 104 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 38 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 0.1980 chunk 81 optimal weight: 30.0000 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 343 GLN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12994 Z= 0.207 Angle : 0.650 12.151 17512 Z= 0.324 Chirality : 0.043 0.155 1998 Planarity : 0.004 0.044 2242 Dihedral : 5.054 27.518 1680 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.21 % Favored : 88.54 % Rotamer: Outliers : 5.07 % Allowed : 28.21 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.20), residues: 1614 helix: -0.55 (0.20), residues: 648 sheet: -0.80 (0.45), residues: 160 loop : -2.02 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 121 HIS 0.005 0.001 HIS B 580 PHE 0.028 0.001 PHE B 454 TYR 0.012 0.001 TYR B 79 ARG 0.008 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 111 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7612 (tt) REVERT: B 637 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6973 (tt) REVERT: B 695 ASN cc_start: 0.7231 (t0) cc_final: 0.6970 (t0) REVERT: A 364 THR cc_start: 0.5293 (OUTLIER) cc_final: 0.4872 (m) REVERT: A 496 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8128 (tt0) REVERT: A 543 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6557 (p0) REVERT: A 668 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7238 (tttt) outliers start: 71 outliers final: 51 residues processed: 171 average time/residue: 0.2206 time to fit residues: 57.4615 Evaluate side-chains 161 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 105 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12994 Z= 0.461 Angle : 0.846 11.682 17512 Z= 0.432 Chirality : 0.049 0.189 1998 Planarity : 0.004 0.051 2242 Dihedral : 5.926 26.806 1680 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.83 % Favored : 86.86 % Rotamer: Outliers : 5.86 % Allowed : 27.79 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.50 (0.20), residues: 1614 helix: -1.19 (0.19), residues: 654 sheet: -0.92 (0.46), residues: 152 loop : -2.22 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 681 HIS 0.008 0.003 HIS B 443 PHE 0.024 0.002 PHE A 327 TYR 0.019 0.002 TYR A 752 ARG 0.005 0.001 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 125 time to evaluate : 1.336 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: B 251 GLU cc_start: 0.7357 (mt-10) cc_final: 0.7050 (mt-10) REVERT: B 341 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7741 (tt) REVERT: B 404 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: B 474 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 610 THR cc_start: 0.7246 (OUTLIER) cc_final: 0.7043 (p) REVERT: B 695 ASN cc_start: 0.7539 (t0) cc_final: 0.7135 (t0) REVERT: A 294 MET cc_start: 0.7422 (ptm) cc_final: 0.7126 (ptt) REVERT: A 364 THR cc_start: 0.5769 (OUTLIER) cc_final: 0.5136 (m) REVERT: A 400 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.7045 (ttm170) REVERT: A 496 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8108 (tt0) REVERT: A 543 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.6717 (p0) REVERT: A 570 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.5881 (tt0) REVERT: A 668 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6963 (tttt) outliers start: 82 outliers final: 53 residues processed: 192 average time/residue: 0.2194 time to fit residues: 64.2920 Evaluate side-chains 168 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12994 Z= 0.278 Angle : 0.718 10.472 17512 Z= 0.367 Chirality : 0.044 0.149 1998 Planarity : 0.004 0.048 2242 Dihedral : 5.554 29.990 1680 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.15 % Favored : 88.54 % Rotamer: Outliers : 4.79 % Allowed : 29.50 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.34 (0.20), residues: 1614 helix: -0.93 (0.19), residues: 646 sheet: -0.98 (0.47), residues: 144 loop : -2.19 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.006 0.002 HIS B 580 PHE 0.021 0.001 PHE B 232 TYR 0.017 0.001 TYR A 355 ARG 0.003 0.001 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 120 time to evaluate : 1.519 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: B 341 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7631 (tt) REVERT: B 359 PHE cc_start: 0.4910 (t80) cc_final: 0.4676 (t80) REVERT: B 371 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7013 (tp30) REVERT: B 453 ASN cc_start: 0.7538 (p0) cc_final: 0.7330 (p0) REVERT: B 474 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6788 (mt-10) REVERT: B 695 ASN cc_start: 0.7321 (t0) cc_final: 0.7061 (t0) REVERT: A 294 MET cc_start: 0.7370 (ptm) cc_final: 0.7000 (ptt) REVERT: A 364 THR cc_start: 0.5418 (OUTLIER) cc_final: 0.4894 (m) REVERT: A 491 VAL cc_start: 0.7858 (p) cc_final: 0.7652 (t) REVERT: A 543 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6536 (p0) REVERT: A 570 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.5800 (tt0) REVERT: A 668 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7002 (tttt) REVERT: A 822 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6256 (mm-30) outliers start: 67 outliers final: 52 residues processed: 178 average time/residue: 0.2053 time to fit residues: 56.3539 Evaluate side-chains 170 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 113 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 143 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12994 Z= 0.266 Angle : 0.722 10.070 17512 Z= 0.366 Chirality : 0.044 0.157 1998 Planarity : 0.004 0.046 2242 Dihedral : 5.436 29.090 1680 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.77 % Favored : 87.92 % Rotamer: Outliers : 4.79 % Allowed : 29.64 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.28 (0.20), residues: 1614 helix: -0.91 (0.19), residues: 658 sheet: -1.04 (0.46), residues: 144 loop : -2.13 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.006 0.001 HIS B 580 PHE 0.018 0.001 PHE B 232 TYR 0.016 0.001 TYR A 355 ARG 0.002 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 123 time to evaluate : 1.365 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: B 341 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7602 (tt) REVERT: B 359 PHE cc_start: 0.4943 (t80) cc_final: 0.4716 (t80) REVERT: B 474 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6796 (mt-10) REVERT: B 695 ASN cc_start: 0.7183 (t0) cc_final: 0.6872 (t0) REVERT: A 294 MET cc_start: 0.7350 (ptm) cc_final: 0.7070 (ptt) REVERT: A 364 THR cc_start: 0.5171 (OUTLIER) cc_final: 0.4628 (m) REVERT: A 450 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6087 (pp) REVERT: A 543 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.6526 (p0) REVERT: A 570 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.5836 (tt0) REVERT: A 668 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6972 (tttt) REVERT: A 822 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6201 (mm-30) outliers start: 67 outliers final: 52 residues processed: 181 average time/residue: 0.2548 time to fit residues: 69.5470 Evaluate side-chains 173 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 115 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 159 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN B 601 ASN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.7221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12994 Z= 0.306 Angle : 0.743 10.299 17512 Z= 0.378 Chirality : 0.045 0.161 1998 Planarity : 0.004 0.049 2242 Dihedral : 5.532 30.457 1680 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.90 % Favored : 87.79 % Rotamer: Outliers : 4.36 % Allowed : 30.00 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.30 (0.20), residues: 1614 helix: -0.96 (0.19), residues: 654 sheet: -1.13 (0.46), residues: 144 loop : -2.09 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.006 0.002 HIS B 580 PHE 0.020 0.002 PHE B 359 TYR 0.021 0.002 TYR A 355 ARG 0.003 0.001 ARG A 839 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 116 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 251 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 341 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7649 (tt) REVERT: B 359 PHE cc_start: 0.4917 (t80) cc_final: 0.4679 (t80) REVERT: B 388 PHE cc_start: 0.7325 (m-80) cc_final: 0.7046 (m-10) REVERT: B 474 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 695 ASN cc_start: 0.7317 (t0) cc_final: 0.7037 (t0) REVERT: A 294 MET cc_start: 0.7409 (ptm) cc_final: 0.7132 (ptt) REVERT: A 304 GLN cc_start: 0.6331 (OUTLIER) cc_final: 0.5932 (tp40) REVERT: A 364 THR cc_start: 0.5240 (OUTLIER) cc_final: 0.4693 (m) REVERT: A 543 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6531 (p0) REVERT: A 570 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.5930 (tt0) REVERT: A 668 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6888 (tttt) outliers start: 61 outliers final: 48 residues processed: 169 average time/residue: 0.1966 time to fit residues: 52.0107 Evaluate side-chains 160 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 106 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 404 PHE Chi-restraints excluded: chain B residue 433 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 721 SER Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 788 SER Chi-restraints excluded: chain B residue 805 TRP Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 858 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.216444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.189974 restraints weight = 18752.800| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 1.84 r_work: 0.4134 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.7241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.458 12994 Z= 0.566 Angle : 1.089 59.169 17512 Z= 0.647 Chirality : 0.049 0.742 1998 Planarity : 0.004 0.095 2242 Dihedral : 5.569 30.355 1680 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.77 % Favored : 87.86 % Rotamer: Outliers : 4.36 % Allowed : 30.00 % Favored : 65.64 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.30 (0.20), residues: 1614 helix: -0.95 (0.19), residues: 654 sheet: -1.13 (0.46), residues: 144 loop : -2.09 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 121 HIS 0.006 0.002 HIS B 580 PHE 0.018 0.002 PHE B 232 TYR 0.019 0.002 TYR A 740 ARG 0.003 0.000 ARG A 839 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2973.70 seconds wall clock time: 54 minutes 43.73 seconds (3283.73 seconds total)