Starting phenix.real_space_refine on Sun Dec 10 00:13:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/12_2023/8a9a_15274.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/12_2023/8a9a_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_15274/12_2023/8a9a_15274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/12_2023/8a9a_15274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/12_2023/8a9a_15274.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a9a_15274/12_2023/8a9a_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.24, per 1000 atoms: 0.57 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: 4.96 Conformation dependent library (CDL) restraints added in 2.7 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: 1.13 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: 3.58 Time building geometry restraints manager: 5.37 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: 9.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 27.950 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.760 Find NCS groups from input model: 0.670 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.150 ------------------------------------------------------------------------------- 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 : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.2761 time to fit residues: 110.5683 Evaluate side-chains 148 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1096 time to fit residues: 2.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 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: 0.6638 ------------------------------------------------------------------------------- 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: 0.6339 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12994 Z= 0.326 Angle : 0.750 10.183 17512 Z= 0.384 Chirality : 0.047 0.211 1998 Planarity : 0.005 0.070 2242 Dihedral : 5.295 25.067 1680 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.90 % Favored : 88.72 % Rotamer: Outliers : 5.79 % Allowed : 25.79 % Favored : 68.43 % 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: -1.86 (0.20), residues: 1614 helix: -0.46 (0.20), residues: 650 sheet: -0.41 (0.47), residues: 132 loop : -2.05 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 681 HIS 0.007 0.002 HIS B 580 PHE 0.021 0.002 PHE B 458 TYR 0.024 0.002 TYR A 623 ARG 0.007 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 231 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 150 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 37 residues processed: 223 average time/residue: 0.2187 time to fit residues: 74.2521 Evaluate side-chains 152 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1167 time to fit residues: 10.1563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 120 optimal weight: 0.2980 chunk 98 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 chunk 144 optimal weight: 0.2980 chunk 49 optimal weight: 0.0870 chunk 116 optimal weight: 0.9980 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 459 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 308 GLN A 431 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12994 Z= 0.197 Angle : 0.631 7.834 17512 Z= 0.320 Chirality : 0.043 0.225 1998 Planarity : 0.004 0.055 2242 Dihedral : 4.934 24.850 1680 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.67 % Favored : 89.96 % Rotamer: Outliers : 2.71 % Allowed : 28.07 % Favored : 69.21 % 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: -1.76 (0.21), residues: 1614 helix: -0.37 (0.20), residues: 660 sheet: -0.46 (0.46), residues: 144 loop : -2.01 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 121 HIS 0.006 0.001 HIS A 580 PHE 0.016 0.001 PHE B 232 TYR 0.017 0.001 TYR B 79 ARG 0.006 0.001 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 173 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 12 residues processed: 170 average time/residue: 0.2326 time to fit residues: 60.3001 Evaluate side-chains 124 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1453 time to fit residues: 5.1326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 245 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 235 ASN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN A 695 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12994 Z= 0.381 Angle : 0.757 9.564 17512 Z= 0.387 Chirality : 0.046 0.160 1998 Planarity : 0.004 0.048 2242 Dihedral : 5.471 25.956 1680 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.08 % Favored : 87.48 % Rotamer: Outliers : 4.21 % Allowed : 27.36 % Favored : 68.43 % 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: -2.19 (0.20), residues: 1614 helix: -0.79 (0.19), residues: 660 sheet: -1.03 (0.43), residues: 160 loop : -2.13 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 681 HIS 0.008 0.003 HIS B 580 PHE 0.020 0.002 PHE B 643 TYR 0.027 0.002 TYR A 623 ARG 0.008 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 189 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 130 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 20 residues processed: 180 average time/residue: 0.2207 time to fit residues: 61.4955 Evaluate side-chains 121 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.552 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1216 time to fit residues: 6.8473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4760 ------------------------------------------------------------------------------- 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 245 ASN A 303 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.5600 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= 0.237 Angle : 0.681 13.767 17512 Z= 0.341 Chirality : 0.044 0.182 1998 Planarity : 0.004 0.044 2242 Dihedral : 5.246 27.670 1680 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.10 % Favored : 89.59 % Rotamer: Outliers : 2.71 % Allowed : 29.21 % 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: -2.06 (0.20), residues: 1614 helix: -0.71 (0.19), residues: 646 sheet: -0.94 (0.44), residues: 160 loop : -2.01 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 805 HIS 0.006 0.002 HIS B 580 PHE 0.023 0.001 PHE B 454 TYR 0.017 0.001 TYR B 79 ARG 0.009 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 163 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 13 residues processed: 158 average time/residue: 0.2467 time to fit residues: 58.6516 Evaluate side-chains 119 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1344 time to fit residues: 5.2604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.3980 chunk 139 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 81 optimal weight: 30.0000 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 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 361 ASN ** B 453 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 305 GLN A 347 GLN ** A 449 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12994 Z= 0.272 Angle : 0.708 12.070 17512 Z= 0.355 Chirality : 0.045 0.170 1998 Planarity : 0.004 0.041 2242 Dihedral : 5.296 27.794 1680 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.71 % Favored : 87.98 % Rotamer: Outliers : 1.64 % Allowed : 30.21 % Favored : 68.14 % 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: -2.11 (0.20), residues: 1614 helix: -0.75 (0.19), residues: 646 sheet: -0.91 (0.45), residues: 160 loop : -2.06 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 121 HIS 0.006 0.002 HIS B 580 PHE 0.021 0.002 PHE B 232 TYR 0.017 0.001 TYR A 623 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 132 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 126 average time/residue: 0.2361 time to fit residues: 45.5939 Evaluate side-chains 109 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1163 time to fit residues: 3.8840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 0.0870 chunk 71 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ** B 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12994 Z= 0.279 Angle : 0.715 10.909 17512 Z= 0.361 Chirality : 0.045 0.196 1998 Planarity : 0.004 0.046 2242 Dihedral : 5.351 27.743 1680 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.21 % Favored : 88.48 % Rotamer: Outliers : 1.43 % Allowed : 30.93 % Favored : 67.64 % 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: -2.23 (0.20), residues: 1614 helix: -0.83 (0.19), residues: 660 sheet: -0.99 (0.44), residues: 160 loop : -2.15 (0.21), residues: 794 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 0.002 PHE B 232 TYR 0.013 0.001 TYR B 79 ARG 0.006 0.001 ARG A 400 *********************** 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 137 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 133 average time/residue: 0.2526 time to fit residues: 50.7856 Evaluate side-chains 115 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1244 time to fit residues: 3.9576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 105 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12994 Z= 0.263 Angle : 0.732 16.073 17512 Z= 0.364 Chirality : 0.045 0.157 1998 Planarity : 0.004 0.046 2242 Dihedral : 5.321 28.707 1680 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.71 % Favored : 87.98 % Rotamer: Outliers : 1.79 % Allowed : 31.36 % Favored : 66.86 % 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: -2.18 (0.20), residues: 1614 helix: -0.80 (0.19), residues: 650 sheet: -0.83 (0.46), residues: 148 loop : -2.12 (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 0.019 0.001 PHE B 232 TYR 0.016 0.001 TYR B 79 ARG 0.009 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 143 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 138 average time/residue: 0.2329 time to fit residues: 49.2740 Evaluate side-chains 114 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1234 time to fit residues: 4.7209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 134 optimal weight: 0.4980 chunk 143 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 129 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 chunk 94 optimal weight: 0.0020 overall best weight: 0.3186 ------------------------------------------------------------------------------- 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 695 ASN B 781 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12994 Z= 0.202 Angle : 0.698 15.208 17512 Z= 0.348 Chirality : 0.043 0.157 1998 Planarity : 0.004 0.043 2242 Dihedral : 5.113 27.968 1680 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.47 % Favored : 89.28 % Rotamer: Outliers : 0.86 % Allowed : 32.00 % Favored : 67.14 % 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: -2.09 (0.20), residues: 1614 helix: -0.68 (0.20), residues: 646 sheet: -0.79 (0.46), residues: 148 loop : -2.11 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 121 HIS 0.010 0.002 HIS A 443 PHE 0.019 0.001 PHE B 232 TYR 0.016 0.001 TYR B 79 ARG 0.004 0.001 ARG A 502 *********************** 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 129 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 127 average time/residue: 0.2451 time to fit residues: 46.8683 Evaluate side-chains 106 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1164 time to fit residues: 2.6178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN ** B 695 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 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.6993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12994 Z= 0.330 Angle : 0.773 15.302 17512 Z= 0.388 Chirality : 0.046 0.177 1998 Planarity : 0.004 0.049 2242 Dihedral : 5.409 28.200 1680 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.21 % Favored : 87.48 % Rotamer: Outliers : 0.43 % Allowed : 32.36 % Favored : 67.21 % 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: -2.24 (0.20), residues: 1614 helix: -0.87 (0.19), residues: 658 sheet: -0.72 (0.46), residues: 148 loop : -2.18 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 681 HIS 0.011 0.003 HIS A 443 PHE 0.024 0.002 PHE B 232 TYR 0.017 0.002 TYR A 355 ARG 0.005 0.001 ARG B 502 ********************** 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 117 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.2433 time to fit residues: 42.6613 Evaluate side-chains 106 residues out of total 1432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1154 time to fit residues: 2.9899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 0.0970 chunk 18 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN ** B 695 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 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.223238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.197535 restraints weight = 18903.420| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.27 r_work: 0.4163 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.7062 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= 0.241 Angle : 0.717 15.123 17512 Z= 0.359 Chirality : 0.044 0.157 1998 Planarity : 0.004 0.048 2242 Dihedral : 5.269 28.631 1680 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.90 % Favored : 88.79 % Rotamer: Outliers : 0.36 % Allowed : 32.29 % Favored : 67.36 % 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: -2.17 (0.20), residues: 1614 helix: -0.74 (0.19), residues: 646 sheet: -0.89 (0.47), residues: 144 loop : -2.14 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 121 HIS 0.010 0.002 HIS A 443 PHE 0.024 0.001 PHE B 232 TYR 0.035 0.001 TYR A 740 ARG 0.004 0.001 ARG A 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.38 seconds wall clock time: 57 minutes 0.32 seconds (3420.32 seconds total)