Starting phenix.real_space_refine on Mon Apr 8 10:48:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8m_41099/04_2024/8t8m_41099_updated.pdb" } 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-5288/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: 7.18, per 1000 atoms: 0.55 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: 5.50 Conformation dependent library (CDL) restraints added in 2.7 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... running ksdssp... Secondary structure from input PDB file: 47 helices and 18 sheets defined 37.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.755A pdb=" N SER A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 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 152 through 165 removed outlier: 4.379A pdb=" N LEU A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N PHE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 196 through 210 removed outlier: 4.496A pdb=" N TYR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.719A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.353A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 415 Processing helix chain 'A' and resid 434 through 441 Processing helix chain 'A' and resid 578 through 603 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 615 through 636 removed outlier: 4.503A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 668 Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 692 through 714 Processing helix chain 'A' and resid 739 through 760 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 770 through 792 Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 801 through 825 Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 67 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 102 through 116 removed outlier: 3.978A pdb=" N SER B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 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 196 through 208 Processing helix chain 'B' and resid 222 through 238 Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.100A pdb=" N HIS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 335 through 343 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) removed outlier: 4.129A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 397 through 418 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 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 578 through 603 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 615 through 633 Processing helix chain 'B' and resid 641 through 670 Proline residue: B 655 - end of helix removed outlier: 3.840A pdb=" N ILE B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 670 " --> pdb=" O THR B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 714 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 737 through 760 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 770 through 792 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 Processing helix chain 'B' and resid 801 through 825 Proline residue: B 820 - end of helix Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing sheet with id= A, 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: 7.021A pdb=" N GLY A 38 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 146 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU A 40 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id= B, 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: 4.325A pdb=" N THR A 219 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N CYS A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU A 302 " --> pdb=" O CYS A 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 325 through 329 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= D, first strand: chain 'A' and resid 445 through 447 Processing sheet with id= E, 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= F, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= G, 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= H, 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: 7.096A pdb=" N GLY B 38 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL B 146 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU B 40 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 245 through 248 removed outlier: 6.636A pdb=" N ALA B 216 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ILE B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS B 218 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU B 302 " --> pdb=" O CYS B 276 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.697A pdb=" N GLY B 485 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN B 470 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN B 483 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS B 472 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR B 481 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 445 through 447 Processing sheet with id= L, first strand: chain 'B' and resid 520 through 524 Processing sheet with id= M, first strand: chain 'B' and resid 719 through 722 Processing sheet with id= N, 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= O, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.275A pdb=" N THR C 122 " --> pdb=" O VAL C 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 119 through 121 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= Q, first strand: chain 'D' and resid 5 through 9 Processing sheet with id= R, first strand: chain 'D' and resid 12 through 15 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) 572 hydrogen bonds defined for protein. 1593 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: 4.87 Time building geometry restraints manager: 5.94 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=" C04 QUS A 901 " pdb=" N14 QUS A 901 " ideal model delta sigma weight residual 1.324 1.439 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C04 QUS B 901 " pdb=" N14 QUS B 901 " ideal model delta sigma weight residual 1.324 1.438 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C05 QUS B 901 " pdb=" N15 QUS B 901 " ideal model delta sigma weight residual 1.331 1.441 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.331 1.440 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C05 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.15e+01 ... (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=" 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 angle pdb=" CA ILE B 642 " pdb=" C ILE B 642 " pdb=" O ILE B 642 " ideal model delta sigma weight residual 121.17 118.26 2.91 1.06e+00 8.90e-01 7.53e+00 angle pdb=" CA ALA B 637 " pdb=" C ALA B 637 " pdb=" O ALA B 637 " ideal model delta sigma weight residual 120.82 117.96 2.86 1.05e+00 9.07e-01 7.40e+00 ... (remaining 18261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7241 17.99 - 35.98: 618 35.98 - 53.98: 97 53.98 - 71.97: 21 71.97 - 89.96: 14 Dihedral angle restraints: 7991 sinusoidal: 2881 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 7988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1510 0.042 - 0.085: 411 0.085 - 0.127: 135 0.127 - 0.169: 8 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: 2354 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 2351 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2167 2.76 - 3.30: 12416 3.30 - 3.83: 20893 3.83 - 4.37: 24267 4.37 - 4.90: 43005 Nonbonded interactions: 102748 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 102743 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 8.720 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 39.050 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.050 ------------------------------------------------------------------------------- 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 : 0.004 0.115 13429 Z= 0.258 Angle : 0.523 7.864 18266 Z= 0.298 Chirality : 0.043 0.212 2067 Planarity : 0.005 0.109 2354 Dihedral : 13.975 89.959 4656 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 : 1.388 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: 1.3908 time to fit residues: 211.4879 Evaluate side-chains 119 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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: 7.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 137 optimal weight: 0.0870 chunk 53 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13429 Z= 0.408 Angle : 0.610 12.416 18266 Z= 0.325 Chirality : 0.046 0.208 2067 Planarity : 0.005 0.079 2354 Dihedral : 5.229 86.927 1898 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.68 % Allowed : 9.31 % Favored : 90.01 % 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: -0.00 (0.20), residues: 1752 helix: 1.69 (0.20), residues: 692 sheet: -0.27 (0.29), residues: 291 loop : -1.52 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 354 HIS 0.006 0.001 HIS B 30 PHE 0.017 0.002 PHE A 818 TYR 0.028 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 129 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.520 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 1.4748 time to fit residues: 197.2527 Evaluate side-chains 122 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 SER 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: 0.8980 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.0785 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= 0.223 Angle : 0.518 14.677 18266 Z= 0.274 Chirality : 0.042 0.168 2067 Planarity : 0.004 0.062 2354 Dihedral : 5.007 86.731 1898 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.14 % Allowed : 11.81 % Favored : 87.06 % 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: 0.16 (0.20), residues: 1752 helix: 1.86 (0.20), residues: 688 sheet: -0.11 (0.29), residues: 291 loop : -1.48 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 354 HIS 0.003 0.001 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.017 0.001 TYR A 223 ARG 0.009 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: 15 poor density : 118 time to evaluate : 1.168 Fit side-chains REVERT: A 524 ARG cc_start: 0.6474 (tmt170) cc_final: 0.6227 (tmt170) REVERT: A 802 MET cc_start: 0.5714 (pmm) cc_final: 0.5492 (pmm) REVERT: B 277 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6709 (t80) REVERT: B 291 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7370 (ttm170) REVERT: B 469 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7278 (mmm) REVERT: C 111 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6597 (mp0) outliers start: 15 outliers final: 5 residues processed: 126 average time/residue: 1.3947 time to fit residues: 191.3790 Evaluate side-chains 123 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 ARG 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 469 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: 0.5980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 0.1980 chunk 169 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.0854 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= 0.215 Angle : 0.509 14.945 18266 Z= 0.268 Chirality : 0.042 0.168 2067 Planarity : 0.004 0.055 2354 Dihedral : 4.918 86.385 1898 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.59 % Allowed : 13.32 % Favored : 85.09 % 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: 1.92 (0.20), residues: 689 sheet: -0.11 (0.29), residues: 305 loop : -1.44 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 354 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.014 0.001 TYR A 223 ARG 0.009 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 139 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.695 Fit side-chains REVERT: A 80 ASN cc_start: 0.8044 (p0) cc_final: 0.7821 (p0) REVERT: A 277 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7481 (t80) REVERT: A 802 MET cc_start: 0.5702 (pmm) cc_final: 0.5481 (pmm) REVERT: B 277 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.6769 (t80) REVERT: B 291 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7384 (ttm170) REVERT: B 469 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7240 (mmm) REVERT: C 111 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6619 (mp0) outliers start: 21 outliers final: 8 residues processed: 130 average time/residue: 1.3726 time to fit residues: 195.0981 Evaluate side-chains 129 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 435 ARG 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 469 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 111 GLU Chi-restraints excluded: chain D residue 111 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 144 optimal weight: 30.0000 chunk 116 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13429 Z= 0.248 Angle : 0.525 15.144 18266 Z= 0.276 Chirality : 0.043 0.169 2067 Planarity : 0.004 0.049 2354 Dihedral : 4.940 86.249 1898 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.82 % Allowed : 14.69 % Favored : 83.50 % 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: 0.23 (0.20), residues: 1752 helix: 1.88 (0.20), residues: 695 sheet: -0.09 (0.29), residues: 305 loop : -1.46 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 354 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 0.009 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 142 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.567 Fit side-chains REVERT: A 80 ASN cc_start: 0.8168 (p0) cc_final: 0.7899 (p0) REVERT: A 277 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7461 (t80) REVERT: A 802 MET cc_start: 0.5711 (pmm) cc_final: 0.5480 (pmm) REVERT: B 277 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6794 (t80) REVERT: B 291 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7486 (ttm170) REVERT: B 469 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7299 (mmm) REVERT: C 111 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6624 (mp0) outliers start: 24 outliers final: 7 residues processed: 132 average time/residue: 1.3608 time to fit residues: 196.7313 Evaluate side-chains 130 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 435 ARG 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 469 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 7.9990 chunk 152 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13429 Z= 0.337 Angle : 0.571 15.249 18266 Z= 0.301 Chirality : 0.044 0.172 2067 Planarity : 0.004 0.054 2354 Dihedral : 5.099 87.093 1898 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.27 % Allowed : 15.44 % Favored : 82.29 % 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: 0.14 (0.20), residues: 1752 helix: 1.83 (0.20), residues: 693 sheet: -0.13 (0.29), residues: 291 loop : -1.49 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.005 0.001 HIS A 218 PHE 0.017 0.002 PHE A 818 TYR 0.019 0.002 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 146 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.483 Fit side-chains REVERT: A 277 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7458 (t80) REVERT: A 802 MET cc_start: 0.5770 (pmm) cc_final: 0.5534 (pmm) REVERT: B 277 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.6833 (t80) REVERT: C 111 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6632 (mp0) outliers start: 30 outliers final: 10 residues processed: 135 average time/residue: 1.2677 time to fit residues: 187.5323 Evaluate side-chains 126 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 PHE 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 266 SER Chi-restraints excluded: chain B residue 277 PHE 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 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: 0.8980 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 95 optimal weight: 0.0070 chunk 142 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 104 optimal weight: 0.3980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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: 0.7800 moved from start: 0.0988 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= 0.172 Angle : 0.498 14.951 18266 Z= 0.261 Chirality : 0.041 0.168 2067 Planarity : 0.003 0.043 2354 Dihedral : 4.846 87.001 1898 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.74 % Allowed : 16.12 % Favored : 82.13 % 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: 0.34 (0.20), residues: 1752 helix: 1.98 (0.20), residues: 690 sheet: -0.01 (0.29), residues: 299 loop : -1.38 (0.22), residues: 763 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 0.013 0.001 TYR B 542 ARG 0.008 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 143 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.556 Fit side-chains REVERT: A 277 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7462 (t80) REVERT: A 802 MET cc_start: 0.5728 (pmm) cc_final: 0.5507 (pmm) REVERT: B 277 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 291 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7298 (ttm170) REVERT: B 293 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8008 (tt) REVERT: C 111 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6584 (mp0) outliers start: 23 outliers final: 8 residues processed: 134 average time/residue: 1.3618 time to fit residues: 199.6572 Evaluate side-chains 130 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 PHE 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 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 293 LEU 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 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: 0.9980 chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 107 optimal weight: 0.0570 chunk 114 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.0770 chunk 153 optimal weight: 6.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- 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 470 ASN ** 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: 0.7759 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13429 Z= 0.132 Angle : 0.473 13.341 18266 Z= 0.246 Chirality : 0.041 0.168 2067 Planarity : 0.003 0.040 2354 Dihedral : 4.619 87.261 1898 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 17.18 % 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: 0.55 (0.20), residues: 1752 helix: 2.17 (0.20), residues: 688 sheet: 0.15 (0.30), residues: 294 loop : -1.28 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.000 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.015 0.001 TYR A 547 ARG 0.010 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 139 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.448 Fit side-chains REVERT: A 72 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7151 (ttt) REVERT: A 277 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7416 (t80) REVERT: A 802 MET cc_start: 0.5712 (pmm) cc_final: 0.5481 (pmm) REVERT: B 277 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.6887 (t80) REVERT: B 291 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7233 (ttm170) REVERT: C 111 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6447 (mp0) outliers start: 19 outliers final: 7 residues processed: 131 average time/residue: 1.3797 time to fit residues: 197.7373 Evaluate side-chains 129 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 435 ARG 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 455 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 0.0370 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 overall best weight: 0.6462 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.1068 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= 0.186 Angle : 0.501 13.012 18266 Z= 0.259 Chirality : 0.041 0.168 2067 Planarity : 0.003 0.047 2354 Dihedral : 4.665 86.843 1898 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.51 % Allowed : 17.71 % Favored : 80.77 % 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: 0.60 (0.20), residues: 1752 helix: 2.23 (0.20), residues: 684 sheet: 0.16 (0.30), residues: 293 loop : -1.24 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 354 HIS 0.004 0.001 HIS A 218 PHE 0.022 0.001 PHE A 544 TYR 0.011 0.001 TYR B 223 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 137 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.501 Fit side-chains REVERT: A 72 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7188 (ttt) REVERT: A 277 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7300 (t80) REVERT: A 802 MET cc_start: 0.5771 (pmm) cc_final: 0.5534 (pmm) REVERT: B 277 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.6899 (t80) REVERT: B 291 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7288 (ttm170) REVERT: B 293 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8017 (tt) REVERT: C 111 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6512 (mp0) outliers start: 20 outliers final: 9 residues processed: 130 average time/residue: 1.3800 time to fit residues: 195.8051 Evaluate side-chains 132 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 312 ASP Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 435 ARG 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 293 LEU 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 166 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 0.0370 chunk 107 optimal weight: 0.0670 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13429 Z= 0.150 Angle : 0.493 12.621 18266 Z= 0.252 Chirality : 0.041 0.174 2067 Planarity : 0.003 0.043 2354 Dihedral : 4.587 87.133 1898 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.36 % Allowed : 17.87 % Favored : 80.77 % 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: 0.65 (0.20), residues: 1752 helix: 2.24 (0.20), residues: 687 sheet: 0.19 (0.30), residues: 294 loop : -1.20 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.000 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.013 0.001 TYR A 547 ARG 0.010 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 136 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.484 Fit side-chains REVERT: A 72 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7206 (ttt) REVERT: A 277 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7363 (t80) REVERT: A 802 MET cc_start: 0.5736 (pmm) cc_final: 0.5475 (pmm) REVERT: B 277 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.6887 (t80) REVERT: B 291 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7192 (ttm170) REVERT: B 293 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7996 (tt) REVERT: B 465 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.7312 (mtm-85) REVERT: C 111 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6442 (mp0) outliers start: 18 outliers final: 9 residues processed: 130 average time/residue: 1.3877 time to fit residues: 196.9302 Evaluate side-chains 133 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 312 ASP Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 435 ARG 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 293 LEU 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: 0.3980 chunk 128 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.174293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.116761 restraints weight = 20317.351| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.86 r_work: 0.3608 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13429 Z= 0.227 Angle : 0.528 12.119 18266 Z= 0.273 Chirality : 0.042 0.176 2067 Planarity : 0.004 0.050 2354 Dihedral : 4.754 86.515 1898 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.59 % Allowed : 17.71 % Favored : 80.70 % 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: 0.56 (0.20), residues: 1752 helix: 2.15 (0.20), residues: 690 sheet: 0.12 (0.30), residues: 299 loop : -1.25 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 354 HIS 0.004 0.001 HIS A 218 PHE 0.021 0.001 PHE A 544 TYR 0.015 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: 4334.59 seconds wall clock time: 78 minutes 34.12 seconds (4714.12 seconds total)