Starting phenix.real_space_refine on Sun Jul 21 04:05:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/07_2024/8t8m_41099.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/07_2024/8t8m_41099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/07_2024/8t8m_41099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/07_2024/8t8m_41099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/07_2024/8t8m_41099.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/07_2024/8t8m_41099.cif" } resolution = 3.0 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 136 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 8306 2.51 5 N 2254 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 315": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13146 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5590 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 230 Chain: "B" Number of atoms: 5660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5660 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 233 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.56, per 1000 atoms: 0.58 Number of scatterers: 13146 At special positions: 0 Unit cell: (109.989, 83.325, 206.646, 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 114 16.00 O 2472 8.00 N 2254 7.00 C 8306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.04 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: 5.44 Conformation dependent library (CDL) restraints added in 2.2 seconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 42.0% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.817A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.684A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.901A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.504A pdb=" N PHE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.900A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 396 through 416 Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 577 through 604 Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.542A pdb=" N SER A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 637 removed outlier: 4.503A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 669 Proline residue: A 655 - end of helix removed outlier: 3.768A pdb=" N ILE A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 715 removed outlier: 3.611A pdb=" N ILE A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'A' and resid 769 through 793 removed outlier: 3.770A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Proline residue: A 790 - end of helix removed outlier: 4.046A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 826 Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.520A pdb=" N SER B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 151 through 165 removed outlier: 3.553A pdb=" N ASN B 160 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.552A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 239 Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.621A pdb=" N PHE B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.846A pdb=" N VAL B 322 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.121A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.683A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.868A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.645A pdb=" N VAL B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 577 through 604 Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.949A pdb=" N SER B 612 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 Processing helix chain 'B' and resid 640 through 669 Proline residue: B 655 - end of helix removed outlier: 3.840A pdb=" N ILE B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 removed outlier: 4.408A pdb=" N LEU B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 761 removed outlier: 3.889A pdb=" N VAL B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.796A pdb=" N ALA B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE B 776 " --> pdb=" O LYS B 772 " (cutoff:3.500A) Proline residue: B 790 - end of helix removed outlier: 3.914A pdb=" N PHE B 793 " --> pdb=" O VAL B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 826 Proline residue: B 820 - end of helix removed outlier: 3.601A pdb=" N LEU B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.967A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.630A pdb=" N SER D 33 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 34 " --> pdb=" O PHE D 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 30 through 34' Processing helix chain 'D' and resid 64 through 67 removed outlier: 3.616A pdb=" N LYS D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.531A pdb=" N THR D 93 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.955A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.901A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.521A pdb=" N THR A 533 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 545 removed outlier: 6.623A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.650A pdb=" N MET B 31 " --> pdb=" O CYS B 93 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 248 removed outlier: 8.021A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB1, first strand: chain 'B' and resid 520 through 524 Processing sheet with id=AB2, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AB4, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.550A pdb=" N LEU C 20 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.894A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG C 40 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.894A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 114 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 9 Processing sheet with id=AB8, first strand: chain 'D' and resid 12 through 15 removed outlier: 6.211A pdb=" N GLY D 12 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER D 124 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 14 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 12 through 15 removed outlier: 6.211A pdb=" N GLY D 12 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER D 124 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 14 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA D 100 " --> pdb=" O ASP D 113 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 5.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2189 1.31 - 1.44: 3600 1.44 - 1.56: 7478 1.56 - 1.69: 0 1.69 - 1.82: 162 Bond restraints: 13429 Sorted by residual: bond pdb=" C05 QUS B 901 " pdb=" N15 QUS B 901 " ideal model delta sigma weight residual 1.365 1.441 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.365 1.440 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C05 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 1.362 1.424 -0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" C05 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 1.362 1.423 -0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" C04 QUS A 901 " pdb=" N14 QUS A 901 " ideal model delta sigma weight residual 1.380 1.439 -0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 13424 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 392 106.97 - 113.74: 7409 113.74 - 120.50: 5087 120.50 - 127.27: 5225 127.27 - 134.03: 153 Bond angle restraints: 18266 Sorted by residual: angle pdb=" C03 QUS A 901 " pdb=" N14 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 112.77 126.56 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C03 QUS B 901 " pdb=" N14 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 112.77 126.36 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N LEU B 567 " pdb=" CA LEU B 567 " pdb=" C LEU B 567 " ideal model delta sigma weight residual 107.88 112.63 -4.75 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C MET B 817 " pdb=" N PHE B 818 " pdb=" CA PHE B 818 " ideal model delta sigma weight residual 122.50 116.94 5.56 1.82e+00 3.02e-01 9.32e+00 angle pdb=" N VAL A 191 " pdb=" CA VAL A 191 " pdb=" C VAL A 191 " ideal model delta sigma weight residual 111.91 109.24 2.67 8.90e-01 1.26e+00 8.98e+00 ... (remaining 18261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7239 17.99 - 35.98: 627 35.98 - 53.98: 101 53.98 - 71.97: 21 71.97 - 89.96: 13 Dihedral angle restraints: 8001 sinusoidal: 2891 harmonic: 5110 Sorted by residual: dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual -86.00 -7.00 -79.00 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual -86.00 -144.99 58.99 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -127.44 41.44 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 7998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1508 0.042 - 0.085: 411 0.085 - 0.127: 136 0.127 - 0.169: 9 0.169 - 0.212: 3 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CB ILE A 636 " pdb=" CA ILE A 636 " pdb=" CG1 ILE A 636 " pdb=" CG2 ILE A 636 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE B 636 " pdb=" N ILE B 636 " pdb=" C ILE B 636 " pdb=" CB ILE B 636 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" CA ILE B 642 " pdb=" N ILE B 642 " pdb=" C ILE B 642 " pdb=" CB ILE B 642 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 2064 not shown) Planarity restraints: 2356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 535 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO A 536 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 430 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO A 431 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 64 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C TYR A 64 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR A 64 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 2353 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2162 2.76 - 3.30: 12377 3.30 - 3.83: 20866 3.83 - 4.37: 24112 4.37 - 4.90: 42971 Nonbonded interactions: 102488 Sorted by model distance: nonbonded pdb=" OH TYR A 311 " pdb=" OD1 ASP A 480 " model vdw 2.230 2.440 nonbonded pdb=" OE1 GLN D 15 " pdb=" OG SER D 124 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR B 559 " pdb=" OD1 ASP B 561 " model vdw 2.310 2.440 nonbonded pdb=" O ARG D 29 " pdb=" OG1 THR D 30 " model vdw 2.323 2.440 nonbonded pdb=" O ASP B 718 " pdb=" N ASN B 734 " model vdw 2.323 2.520 ... (remaining 102483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 297 or (resid 298 and (name N or n \ ame CA or name C or name O or name CB )) or resid 299 through 490 or (resid 491 \ and (name N or name CA or name C or name O or name CB )) or resid 492 through 52 \ 3 or (resid 524 and (name N or name CA or name C or name O or name CB )) or resi \ d 525 through 545 or (resid 546 through 547 and (name N or name CA or name C or \ name O or name CB )) or resid 548 through 634 or (resid 635 through 638 and (nam \ e N or name CA or name C or name O or name CB )) or resid 639 through 826 or res \ id 901)) selection = (chain 'B' and (resid 25 through 417 or resid 428 through 501 or (resid 502 thro \ ugh 503 and (name N or name CA or name C or name O or name CB )) or resid 504 th \ rough 507 or (resid 508 and (name N or name CA or name C or name O or name CB )) \ or resid 509 through 512 or (resid 513 and (name N or name CA or name C or name \ O or name CB )) or resid 514 through 516 or (resid 517 and (name N or name CA o \ r name C or name O or name CB )) or resid 518 or (resid 519 and (name N or name \ CA or name C or name O or name CB )) or resid 520 through 541 or (resid 542 and \ (name N or name CA or name C or name O or name CB )) or resid 543 through 552 or \ (resid 553 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 4 through 566 or (resid 567 and (name N or name CA or name C or name O or name C \ B )) or resid 568 through 826 or resid 901)) } ncs_group { reference = (chain 'C' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) selection = chain 'D' } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 37.090 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 0.076 13429 Z= 0.207 Angle : 0.563 13.792 18266 Z= 0.306 Chirality : 0.043 0.212 2067 Planarity : 0.005 0.109 2356 Dihedral : 14.005 89.959 4666 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1752 helix: 1.71 (0.20), residues: 686 sheet: -0.05 (0.30), residues: 294 loop : -1.41 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.019 0.001 PHE A 818 TYR 0.016 0.001 TYR A 223 ARG 0.008 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.392 Fit side-chains REVERT: A 524 ARG cc_start: 0.6176 (ttt-90) cc_final: 0.5781 (tpt-90) REVERT: C 85 MET cc_start: 0.7211 (mtt) cc_final: 0.6981 (mtp) REVERT: D 36 MET cc_start: 0.8451 (mmm) cc_final: 0.8140 (mmp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 1.2907 time to fit residues: 195.9290 Evaluate side-chains 119 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 137 optimal weight: 0.0870 chunk 53 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13429 Z= 0.398 Angle : 0.627 13.006 18266 Z= 0.332 Chirality : 0.046 0.205 2067 Planarity : 0.005 0.077 2356 Dihedral : 5.429 79.609 1908 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.83 % Allowed : 9.24 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1752 helix: 1.90 (0.20), residues: 691 sheet: -0.27 (0.29), residues: 285 loop : -1.52 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 336 HIS 0.006 0.001 HIS B 30 PHE 0.017 0.002 PHE A 818 TYR 0.026 0.002 TYR A 223 ARG 0.008 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.511 Fit side-chains REVERT: A 72 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7700 (ttt) REVERT: B 291 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7823 (ttm170) outliers start: 11 outliers final: 4 residues processed: 124 average time/residue: 1.3582 time to fit residues: 183.4190 Evaluate side-chains 123 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 0.0870 chunk 54 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13429 Z= 0.272 Angle : 0.554 14.204 18266 Z= 0.292 Chirality : 0.043 0.170 2067 Planarity : 0.004 0.062 2356 Dihedral : 5.207 87.462 1908 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.29 % Allowed : 12.49 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1752 helix: 2.09 (0.20), residues: 688 sheet: -0.17 (0.29), residues: 285 loop : -1.56 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.016 0.001 TYR B 223 ARG 0.008 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.417 Fit side-chains REVERT: A 72 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7637 (ttt) REVERT: A 802 MET cc_start: 0.5793 (pmm) cc_final: 0.5573 (pmm) REVERT: B 277 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.6767 (t80) REVERT: B 291 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7709 (ttm170) REVERT: C 111 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6656 (mp0) outliers start: 17 outliers final: 4 residues processed: 124 average time/residue: 1.4992 time to fit residues: 202.5317 Evaluate side-chains 122 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 111 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 151 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13429 Z= 0.187 Angle : 0.512 14.998 18266 Z= 0.267 Chirality : 0.042 0.169 2067 Planarity : 0.004 0.055 2356 Dihedral : 4.902 87.576 1908 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.67 % Allowed : 14.16 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1752 helix: 2.29 (0.20), residues: 690 sheet: -0.05 (0.29), residues: 293 loop : -1.50 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.014 0.001 TYR B 542 ARG 0.008 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.569 Fit side-chains REVERT: A 72 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7627 (ttt) REVERT: A 80 ASN cc_start: 0.8005 (p0) cc_final: 0.7791 (p0) REVERT: A 277 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7425 (t80) REVERT: A 802 MET cc_start: 0.5726 (pmm) cc_final: 0.5502 (pmm) REVERT: B 72 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7723 (ttt) REVERT: B 228 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7984 (mmp) REVERT: B 277 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6791 (t80) REVERT: C 111 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6614 (mp0) outliers start: 22 outliers final: 6 residues processed: 131 average time/residue: 1.2616 time to fit residues: 181.4648 Evaluate side-chains 126 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 144 optimal weight: 30.0000 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13429 Z= 0.227 Angle : 0.528 15.059 18266 Z= 0.275 Chirality : 0.042 0.169 2067 Planarity : 0.004 0.050 2356 Dihedral : 4.907 86.212 1908 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.20 % Allowed : 14.84 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1752 helix: 2.32 (0.20), residues: 694 sheet: 0.04 (0.30), residues: 279 loop : -1.48 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE A 544 TYR 0.015 0.001 TYR B 223 ARG 0.010 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.394 Fit side-chains REVERT: A 72 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7641 (ttt) REVERT: A 80 ASN cc_start: 0.8096 (p0) cc_final: 0.7853 (p0) REVERT: A 277 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7407 (t80) REVERT: A 802 MET cc_start: 0.5738 (pmm) cc_final: 0.5498 (pmm) REVERT: B 72 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7752 (ttt) REVERT: B 277 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6798 (t80) REVERT: B 291 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7463 (ttm170) REVERT: C 111 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6620 (mp0) outliers start: 29 outliers final: 9 residues processed: 134 average time/residue: 1.2331 time to fit residues: 182.2233 Evaluate side-chains 133 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13429 Z= 0.302 Angle : 0.564 14.469 18266 Z= 0.296 Chirality : 0.044 0.169 2067 Planarity : 0.004 0.055 2356 Dihedral : 5.107 86.822 1908 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.04 % Allowed : 15.59 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1752 helix: 2.24 (0.20), residues: 693 sheet: -0.09 (0.29), residues: 285 loop : -1.50 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS A 218 PHE 0.017 0.001 PHE A 818 TYR 0.018 0.001 TYR B 223 ARG 0.011 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.426 Fit side-chains REVERT: A 72 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7634 (ttt) REVERT: A 277 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7500 (t80) REVERT: A 802 MET cc_start: 0.5764 (pmm) cc_final: 0.5524 (pmm) REVERT: B 72 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7851 (ttt) REVERT: B 277 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.6842 (t80) REVERT: B 291 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7593 (ttm170) REVERT: C 111 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6611 (mp0) outliers start: 27 outliers final: 8 residues processed: 133 average time/residue: 1.2742 time to fit residues: 185.5043 Evaluate side-chains 128 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 0.0370 chunk 104 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13429 Z= 0.166 Angle : 0.502 13.994 18266 Z= 0.261 Chirality : 0.041 0.169 2067 Planarity : 0.004 0.044 2356 Dihedral : 4.751 84.978 1908 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.89 % Allowed : 16.73 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1752 helix: 2.40 (0.20), residues: 696 sheet: 0.06 (0.30), residues: 281 loop : -1.45 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.021 0.001 PHE A 544 TYR 0.012 0.001 TYR B 542 ARG 0.009 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.305 Fit side-chains REVERT: A 72 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7586 (ttt) REVERT: A 802 MET cc_start: 0.5744 (pmm) cc_final: 0.5495 (pmm) REVERT: B 72 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7721 (ttt) REVERT: B 228 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7961 (mmp) REVERT: B 277 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.6820 (t80) REVERT: B 291 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7360 (ttm170) REVERT: C 111 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6569 (mp0) outliers start: 25 outliers final: 12 residues processed: 131 average time/residue: 1.3079 time to fit residues: 187.2283 Evaluate side-chains 134 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 106 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13429 Z= 0.197 Angle : 0.516 13.269 18266 Z= 0.269 Chirality : 0.042 0.169 2067 Planarity : 0.004 0.046 2356 Dihedral : 4.737 83.584 1908 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.04 % Allowed : 17.49 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.20), residues: 1752 helix: 2.42 (0.20), residues: 696 sheet: 0.07 (0.30), residues: 281 loop : -1.43 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.017 0.001 PHE A 818 TYR 0.012 0.001 TYR B 223 ARG 0.011 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 1.513 Fit side-chains REVERT: A 72 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7640 (ttt) REVERT: A 802 MET cc_start: 0.5611 (pmm) cc_final: 0.5360 (pmm) REVERT: B 72 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7739 (ttt) REVERT: B 277 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.6832 (t80) REVERT: B 291 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7459 (ttm170) REVERT: C 111 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6605 (mp0) outliers start: 27 outliers final: 12 residues processed: 133 average time/residue: 1.2433 time to fit residues: 181.1029 Evaluate side-chains 133 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.4980 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13429 Z= 0.201 Angle : 0.522 12.387 18266 Z= 0.271 Chirality : 0.042 0.170 2067 Planarity : 0.004 0.046 2356 Dihedral : 4.705 82.691 1908 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.74 % Allowed : 18.02 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1752 helix: 2.44 (0.20), residues: 696 sheet: 0.09 (0.30), residues: 281 loop : -1.42 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.023 0.001 PHE A 544 TYR 0.013 0.001 TYR D 103 ARG 0.011 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.371 Fit side-chains REVERT: A 72 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7633 (ttt) REVERT: A 802 MET cc_start: 0.5622 (pmm) cc_final: 0.5361 (pmm) REVERT: B 72 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7747 (ttt) REVERT: B 277 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.6767 (t80) REVERT: B 291 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7450 (ttm170) REVERT: C 111 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6576 (mp0) outliers start: 23 outliers final: 11 residues processed: 129 average time/residue: 1.2957 time to fit residues: 182.4444 Evaluate side-chains 132 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 174 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13429 Z= 0.190 Angle : 0.528 13.197 18266 Z= 0.271 Chirality : 0.042 0.173 2067 Planarity : 0.004 0.047 2356 Dihedral : 4.648 81.077 1908 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.36 % Allowed : 18.47 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1752 helix: 2.47 (0.20), residues: 696 sheet: 0.07 (0.30), residues: 293 loop : -1.39 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.026 0.001 PHE A 544 TYR 0.012 0.001 TYR B 542 ARG 0.011 0.000 ARG A 465 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.397 Fit side-chains REVERT: A 72 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7610 (ttt) REVERT: A 802 MET cc_start: 0.5587 (pmm) cc_final: 0.5299 (pmm) REVERT: B 72 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7717 (ttt) REVERT: B 228 MET cc_start: 0.8600 (tpp) cc_final: 0.8113 (mmp) REVERT: B 277 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.6769 (t80) REVERT: B 291 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: C 111 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6565 (mp0) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 1.4126 time to fit residues: 195.7176 Evaluate side-chains 133 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 10.0000 chunk 42 optimal weight: 0.0070 chunk 128 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 122 optimal weight: 0.0040 overall best weight: 0.7412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.175777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.118792 restraints weight = 20456.385| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.73 r_work: 0.3676 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13429 Z= 0.198 Angle : 0.531 12.152 18266 Z= 0.273 Chirality : 0.042 0.174 2067 Planarity : 0.004 0.046 2356 Dihedral : 4.651 80.326 1908 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.59 % Allowed : 18.24 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1752 helix: 2.55 (0.20), residues: 690 sheet: 0.14 (0.30), residues: 277 loop : -1.35 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.012 0.001 TYR B 223 ARG 0.011 0.000 ARG A 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4053.97 seconds wall clock time: 71 minutes 57.00 seconds (4317.00 seconds total)