Starting phenix.real_space_refine on Wed Feb 14 16:40:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2y_21534/02_2024/6w2y_21534_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2y_21534/02_2024/6w2y_21534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2y_21534/02_2024/6w2y_21534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2y_21534/02_2024/6w2y_21534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2y_21534/02_2024/6w2y_21534_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w2y_21534/02_2024/6w2y_21534_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 43 5.16 5 Cl 4 4.86 5 C 6322 2.51 5 N 1620 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 619": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9721 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4731 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 635} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 730 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 351 Chain: "B" Number of atoms: 4734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 4734 Classifications: {'peptide': 664} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 636} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 580 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 480 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 2, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 16, 'PHE:plan': 4, 'GLU:plan': 22, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 365 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Unusual residues: {' MG': 1, 'L9Q': 1, 'NAG': 2, 'SGG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N L9Q A 906 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q A 906 " occ=0.99 residue: pdb=" N L9Q B 906 " occ=0.99 ... (44 atoms not shown) pdb=" P L9Q B 906 " occ=0.99 Time building chain proxies: 6.05, per 1000 atoms: 0.62 Number of scatterers: 9721 At special positions: 0 Unit cell: (116.6, 75.26, 162.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 43 16.00 P 4 15.00 Mg 2 11.99 O 1726 8.00 N 1620 7.00 C 6322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 129 " distance=2.05 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 129 " distance=2.05 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 644 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 901 " - " ASN A 365 " " NAG B 901 " - " ASN B 397 " " NAG C 1 " - " ASN A 323 " " NAG D 1 " - " ASN B 323 " Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2494 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 10 sheets defined 46.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.621A pdb=" N THR A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 111 " --> pdb=" O GLN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 174 through 187 Proline residue: A 178 - end of helix removed outlier: 4.238A pdb=" N VAL A 181 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU A 185 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 186 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.629A pdb=" N LEU A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.822A pdb=" N CYS A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.814A pdb=" N GLU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 367 removed outlier: 3.953A pdb=" N THR A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 474 through 497 Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 510 through 529 removed outlier: 4.102A pdb=" N LEU A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Proline residue: A 529 - end of helix Processing helix chain 'A' and resid 542 through 573 removed outlier: 4.029A pdb=" N LEU A 550 " --> pdb=" O CYS A 546 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 568 " --> pdb=" O MET A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 614 removed outlier: 4.153A pdb=" N VAL A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 673 Processing helix chain 'A' and resid 687 through 711 removed outlier: 4.323A pdb=" N ALA A 703 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Proline residue: A 704 - end of helix removed outlier: 4.098A pdb=" N SER A 710 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER A 711 " --> pdb=" O ILE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 735 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.812A pdb=" N LYS B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 111 " --> pdb=" O GLN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 174 through 187 Proline residue: B 178 - end of helix removed outlier: 3.966A pdb=" N VAL B 181 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU B 185 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 186 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.602A pdb=" N LEU B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.751A pdb=" N CYS B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 326 through 336 removed outlier: 3.908A pdb=" N GLU B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 367 removed outlier: 3.949A pdb=" N THR B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 474 through 498 Processing helix chain 'B' and resid 503 through 506 No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 510 through 531 removed outlier: 4.197A pdb=" N LEU B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 527 " --> pdb=" O ALA B 523 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N PHE B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing helix chain 'B' and resid 542 through 574 removed outlier: 4.130A pdb=" N LEU B 550 " --> pdb=" O CYS B 546 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 614 removed outlier: 3.771A pdb=" N THR B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 601 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 673 Processing helix chain 'B' and resid 686 through 711 Proline residue: B 704 - end of helix removed outlier: 3.614A pdb=" N SER B 710 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER B 711 " --> pdb=" O MET B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 743 removed outlier: 4.376A pdb=" N LEU B 735 " --> pdb=" O THR B 731 " (cutoff:3.500A) Proline residue: B 738 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 92 through 100 removed outlier: 6.462A pdb=" N ARG A 51 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYS A 95 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 53 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 97 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 55 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS A 99 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 57 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 149 Processing sheet with id= C, first strand: chain 'A' and resid 222 through 226 removed outlier: 3.886A pdb=" N GLN A 196 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 272 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY A 247 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 274 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 306 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN A 424 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS A 432 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 400 through 403 removed outlier: 3.717A pdb=" N PHE A 401 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 463 through 467 removed outlier: 6.391A pdb=" N SER A 636 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 466 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU A 638 " --> pdb=" O THR A 466 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 92 through 100 removed outlier: 6.453A pdb=" N ARG B 51 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS B 95 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 53 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE B 97 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 55 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N HIS B 99 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 57 " --> pdb=" O HIS B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 147 through 149 Processing sheet with id= H, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.405A pdb=" N VAL B 272 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY B 247 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE B 274 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 308 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 463 through 468 removed outlier: 6.359A pdb=" N SER B 636 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR B 466 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 638 " --> pdb=" O THR B 466 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG B 468 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN B 640 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 419 through 425 removed outlier: 3.590A pdb=" N ILE B 422 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLY B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN B 424 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LYS B 432 " --> pdb=" O GLN B 424 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1533 1.32 - 1.45: 3079 1.45 - 1.59: 5255 1.59 - 1.72: 4 1.72 - 1.86: 74 Bond restraints: 9945 Sorted by residual: bond pdb=" CA SER A 152 " pdb=" CB SER A 152 " ideal model delta sigma weight residual 1.530 1.455 0.075 1.43e-02 4.89e+03 2.74e+01 bond pdb=" C SER A 149 " pdb=" O SER A 149 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.20e-02 6.94e+03 1.67e+01 bond pdb=" CA SER A 153 " pdb=" CB SER A 153 " ideal model delta sigma weight residual 1.528 1.467 0.060 1.82e-02 3.02e+03 1.10e+01 bond pdb=" C TYR A 150 " pdb=" O TYR A 150 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.38e-02 5.25e+03 1.03e+01 bond pdb=" C13 SGG B 907 " pdb="CL1 SGG B 907 " ideal model delta sigma weight residual 1.724 1.785 -0.061 2.00e-02 2.50e+03 9.32e+00 ... (remaining 9940 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.46: 182 105.46 - 112.64: 5383 112.64 - 119.82: 3078 119.82 - 127.00: 4803 127.00 - 134.18: 142 Bond angle restraints: 13588 Sorted by residual: angle pdb=" C GLY A 277 " pdb=" N TRP A 278 " pdb=" CA TRP A 278 " ideal model delta sigma weight residual 120.28 127.51 -7.23 1.44e+00 4.82e-01 2.52e+01 angle pdb=" CA SER A 149 " pdb=" C SER A 149 " pdb=" O SER A 149 " ideal model delta sigma weight residual 120.70 115.80 4.90 1.15e+00 7.56e-01 1.82e+01 angle pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" O4 NAG A 901 " ideal model delta sigma weight residual 107.29 119.69 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CA SER A 152 " pdb=" C SER A 152 " pdb=" O SER A 152 " ideal model delta sigma weight residual 120.43 116.00 4.43 1.09e+00 8.42e-01 1.65e+01 angle pdb=" CA ASP B 281 " pdb=" C ASP B 281 " pdb=" O ASP B 281 " ideal model delta sigma weight residual 121.19 116.98 4.21 1.10e+00 8.26e-01 1.47e+01 ... (remaining 13583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 5626 25.98 - 51.95: 244 51.95 - 77.93: 21 77.93 - 103.91: 8 103.91 - 129.88: 7 Dihedral angle restraints: 5906 sinusoidal: 2053 harmonic: 3853 Sorted by residual: dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 129 " pdb=" CB CYS B 129 " ideal model delta sinusoidal sigma weight residual 93.00 18.54 74.46 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS A 103 " pdb=" SG CYS A 103 " pdb=" SG CYS A 129 " pdb=" CB CYS A 129 " ideal model delta sinusoidal sigma weight residual 93.00 41.91 51.09 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" C21 L9Q B 906 " pdb=" C22 L9Q B 906 " pdb=" C23 L9Q B 906 " pdb=" C24 L9Q B 906 " ideal model delta sinusoidal sigma weight residual 179.52 -50.60 -129.88 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 5903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 1617 0.310 - 0.620: 2 0.620 - 0.930: 0 0.930 - 1.240: 0 1.240 - 1.550: 1 Chirality restraints: 1620 Sorted by residual: chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.98 -1.55 2.00e-01 2.50e+01 6.01e+01 chirality pdb=" C2 NAG A 901 " pdb=" C1 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" N2 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.49 -1.95 -0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" C2 L9Q B 906 " pdb=" C1 L9Q B 906 " pdb=" C3 L9Q B 906 " pdb=" O2 L9Q B 906 " both_signs ideal model delta sigma weight residual False 2.36 1.97 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1617 not shown) Planarity restraints: 1695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 307 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C THR B 307 " -0.070 2.00e-02 2.50e+03 pdb=" O THR B 307 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 308 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 150 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C TYR A 150 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR A 150 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 151 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 126 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO A 127 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " -0.039 5.00e-02 4.00e+02 ... (remaining 1692 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 833 2.73 - 3.28: 10271 3.28 - 3.82: 15852 3.82 - 4.36: 18966 4.36 - 4.90: 32726 Nonbonded interactions: 78648 Sorted by model distance: nonbonded pdb=" O GLY A 277 " pdb="MG MG A 905 " model vdw 2.193 2.170 nonbonded pdb=" OD2 ASP A 355 " pdb=" OG SER A 405 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR A 117 " pdb=" OE2 GLU B 114 " model vdw 2.218 2.440 nonbonded pdb=" O PHE A 184 " pdb=" N GLY A 188 " model vdw 2.228 2.520 nonbonded pdb=" OH TYR A 113 " pdb=" OG1 THR B 109 " model vdw 2.242 2.440 ... (remaining 78643 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 49 through 225 or (resid 226 and (name N or name CA or nam \ e C or name O or name CB )) or resid 227 through 250 or (resid 251 through 254 a \ nd (name N or name CA or name C or name O or name CB )) or resid 255 through 280 \ or (resid 281 through 282 and (name N or name CA or name C or name O or name CB \ )) or resid 283 through 306 or (resid 307 through 308 and (name N or name CA or \ name C or name O or name CB )) or resid 309 through 354 or (resid 355 through 3 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 357 through \ 425 or (resid 426 and (name N or name CA or name C or name O or name CB )) or r \ esid 427 through 443 or (resid 444 and (name N or name CA or name C or name O or \ name CB )) or resid 445 through 648 or (resid 649 and (name N or name CA or nam \ e C or name O or name CB )) or resid 650 through 744 or resid 901 through 907)) selection = (chain 'B' and (resid 49 through 220 or (resid 221 and (name N or name CA or nam \ e C or name O or name CB )) or resid 222 through 307 or (resid 308 and (name N o \ r name CA or name C or name O or name CB )) or resid 309 through 343 or (resid 3 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 345 through \ 408 or (resid 409 and (name N or name CA or name C or name O or name CB )) or r \ esid 410 through 461 or (resid 462 through 466 and (name N or name CA or name C \ or name O or name CB )) or resid 467 through 477 or (resid 478 and (name N or na \ me CA or name C or name O or name CB )) or resid 479 through 494 or (resid 495 a \ nd (name N or name CA or name C or name O or name CB )) or resid 496 through 544 \ or (resid 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 570 or (resid 571 and (name N or name CA or name C or name O or nam \ e CB )) or resid 572 through 676 or resid 683 through 744 or resid 901 through 9 \ 07)) } ncs_group { reference = chain 'C' 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=0.99 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.870 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.030 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.007 0.075 9945 Z= 0.476 Angle : 0.735 12.396 13588 Z= 0.386 Chirality : 0.063 1.550 1620 Planarity : 0.005 0.072 1691 Dihedral : 14.891 129.881 3394 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.12 % Allowed : 14.85 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -3.95 (0.19), residues: 1307 helix: -1.99 (0.17), residues: 666 sheet: -2.60 (0.31), residues: 210 loop : -3.36 (0.23), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 278 HIS 0.005 0.001 HIS B 305 PHE 0.015 0.001 PHE A 226 TYR 0.027 0.002 TYR A 150 ARG 0.003 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: B 121 ILE cc_start: 0.8701 (mt) cc_final: 0.8484 (tt) REVERT: B 190 LYS cc_start: 0.8174 (mptt) cc_final: 0.7852 (mmtm) REVERT: B 419 TRP cc_start: 0.7683 (m-10) cc_final: 0.7239 (m100) REVERT: B 481 LEU cc_start: 0.7624 (mp) cc_final: 0.7380 (mp) outliers start: 1 outliers final: 1 residues processed: 165 average time/residue: 0.2179 time to fit residues: 50.2329 Evaluate side-chains 114 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 62 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 176 HIS A 305 HIS A 348 GLN A 694 ASN B 99 HIS ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 365 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9945 Z= 0.193 Angle : 0.583 9.631 13588 Z= 0.285 Chirality : 0.042 0.161 1620 Planarity : 0.004 0.042 1691 Dihedral : 10.136 120.792 1677 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.16 % Allowed : 15.09 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.05 (0.22), residues: 1307 helix: -0.55 (0.19), residues: 684 sheet: -1.94 (0.34), residues: 205 loop : -2.20 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.005 0.001 HIS A 305 PHE 0.012 0.001 PHE B 495 TYR 0.024 0.002 TYR A 113 ARG 0.004 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.014 Fit side-chains REVERT: A 286 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7107 (mp) REVERT: A 298 MET cc_start: 0.7528 (mmm) cc_final: 0.7185 (mmt) REVERT: B 121 ILE cc_start: 0.8785 (mt) cc_final: 0.8563 (tt) REVERT: B 190 LYS cc_start: 0.8154 (mptt) cc_final: 0.7865 (mmtm) REVERT: B 419 TRP cc_start: 0.7670 (m-10) cc_final: 0.7349 (m100) outliers start: 18 outliers final: 9 residues processed: 149 average time/residue: 0.1893 time to fit residues: 41.1144 Evaluate side-chains 120 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 545 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 119 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 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 511 ASN ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9945 Z= 0.259 Angle : 0.567 8.131 13588 Z= 0.279 Chirality : 0.043 0.181 1620 Planarity : 0.004 0.044 1691 Dihedral : 9.368 115.217 1675 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.63 % Allowed : 17.60 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.36 (0.23), residues: 1307 helix: -0.05 (0.20), residues: 686 sheet: -1.67 (0.34), residues: 209 loop : -1.72 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 445 HIS 0.003 0.001 HIS B 305 PHE 0.013 0.001 PHE A 226 TYR 0.018 0.002 TYR A 113 ARG 0.003 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.022 Fit side-chains REVERT: A 262 TYR cc_start: 0.6891 (t80) cc_final: 0.6630 (t80) REVERT: A 298 MET cc_start: 0.7600 (mmm) cc_final: 0.7032 (mmt) REVERT: B 76 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7182 (mt-10) REVERT: B 411 ASP cc_start: 0.7631 (p0) cc_final: 0.7277 (p0) REVERT: B 419 TRP cc_start: 0.7739 (m-10) cc_final: 0.7360 (m100) outliers start: 22 outliers final: 13 residues processed: 139 average time/residue: 0.2119 time to fit residues: 43.3662 Evaluate side-chains 124 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.6476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9945 Z= 0.228 Angle : 0.546 7.422 13588 Z= 0.266 Chirality : 0.042 0.156 1620 Planarity : 0.004 0.044 1691 Dihedral : 8.817 104.512 1675 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.71 % Allowed : 17.01 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.93 (0.23), residues: 1307 helix: 0.28 (0.20), residues: 683 sheet: -1.48 (0.34), residues: 209 loop : -1.48 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 419 HIS 0.004 0.001 HIS A 305 PHE 0.011 0.001 PHE A 226 TYR 0.016 0.001 TYR A 113 ARG 0.003 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.319 Fit side-chains REVERT: A 286 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7223 (mp) REVERT: A 298 MET cc_start: 0.7625 (mmm) cc_final: 0.7353 (mmt) REVERT: A 650 ASN cc_start: 0.7480 (m-40) cc_final: 0.6857 (p0) REVERT: B 76 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7303 (mt-10) REVERT: B 419 TRP cc_start: 0.7706 (m-10) cc_final: 0.7303 (m100) REVERT: B 551 TRP cc_start: 0.7893 (m100) cc_final: 0.7389 (m100) REVERT: B 722 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7757 (mm) outliers start: 31 outliers final: 19 residues processed: 148 average time/residue: 0.1876 time to fit residues: 41.4126 Evaluate side-chains 130 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9945 Z= 0.367 Angle : 0.620 8.011 13588 Z= 0.305 Chirality : 0.045 0.230 1620 Planarity : 0.004 0.041 1691 Dihedral : 8.872 103.314 1675 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.19 % Allowed : 18.44 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.99 (0.23), residues: 1307 helix: 0.21 (0.20), residues: 688 sheet: -1.59 (0.34), residues: 210 loop : -1.41 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 419 HIS 0.005 0.001 HIS B 305 PHE 0.021 0.002 PHE A 226 TYR 0.021 0.002 TYR A 113 ARG 0.004 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8511 (mmm) cc_final: 0.8236 (mmm) REVERT: A 262 TYR cc_start: 0.6595 (t80) cc_final: 0.6365 (t80) REVERT: A 286 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7260 (mp) REVERT: A 298 MET cc_start: 0.7838 (mmm) cc_final: 0.7510 (mmt) REVERT: B 419 TRP cc_start: 0.7699 (m-10) cc_final: 0.7253 (m100) REVERT: B 722 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7846 (mm) outliers start: 35 outliers final: 19 residues processed: 146 average time/residue: 0.1898 time to fit residues: 41.3678 Evaluate side-chains 130 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 400 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 618 HIS Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 0.0370 chunk 59 optimal weight: 0.0370 chunk 10 optimal weight: 0.0000 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 overall best weight: 0.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9945 Z= 0.173 Angle : 0.543 8.849 13588 Z= 0.264 Chirality : 0.041 0.189 1620 Planarity : 0.004 0.035 1691 Dihedral : 8.469 94.299 1675 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.75 % Allowed : 19.52 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.58 (0.23), residues: 1307 helix: 0.55 (0.21), residues: 678 sheet: -1.36 (0.35), residues: 210 loop : -1.22 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 419 HIS 0.004 0.001 HIS B 305 PHE 0.010 0.001 PHE A 284 TYR 0.014 0.001 TYR B 561 ARG 0.003 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8471 (mmm) cc_final: 0.8211 (mmm) REVERT: A 243 ARG cc_start: 0.7701 (mtp85) cc_final: 0.6872 (mtt90) REVERT: A 650 ASN cc_start: 0.7508 (m-40) cc_final: 0.6856 (p0) REVERT: B 419 TRP cc_start: 0.7647 (m-10) cc_final: 0.7249 (m100) REVERT: B 722 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7878 (mm) outliers start: 23 outliers final: 17 residues processed: 141 average time/residue: 0.1823 time to fit residues: 37.9227 Evaluate side-chains 135 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9945 Z= 0.250 Angle : 0.562 12.245 13588 Z= 0.272 Chirality : 0.042 0.187 1620 Planarity : 0.004 0.036 1691 Dihedral : 8.345 91.492 1675 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.83 % Allowed : 18.32 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.51 (0.24), residues: 1307 helix: 0.61 (0.21), residues: 678 sheet: -1.36 (0.34), residues: 211 loop : -1.16 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.015 0.001 PHE A 226 TYR 0.023 0.001 TYR A 113 ARG 0.002 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8503 (mmm) cc_final: 0.8233 (mmm) REVERT: A 286 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7359 (mp) REVERT: A 650 ASN cc_start: 0.7479 (m-40) cc_final: 0.6902 (p0) REVERT: B 419 TRP cc_start: 0.7687 (m-10) cc_final: 0.7267 (m100) REVERT: B 722 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (mm) outliers start: 32 outliers final: 20 residues processed: 149 average time/residue: 0.1696 time to fit residues: 38.4055 Evaluate side-chains 132 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.0020 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.0050 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9945 Z= 0.195 Angle : 0.569 16.589 13588 Z= 0.268 Chirality : 0.042 0.242 1620 Planarity : 0.004 0.034 1691 Dihedral : 8.040 89.331 1675 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.11 % Allowed : 19.40 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.37 (0.24), residues: 1307 helix: 0.68 (0.21), residues: 687 sheet: -1.31 (0.35), residues: 211 loop : -1.07 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.008 0.001 PHE A 284 TYR 0.019 0.001 TYR A 113 ARG 0.002 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7661 (mtp85) cc_final: 0.6824 (mtt90) REVERT: A 286 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 650 ASN cc_start: 0.7453 (m-40) cc_final: 0.6883 (p0) REVERT: B 419 TRP cc_start: 0.7691 (m-10) cc_final: 0.7257 (m100) REVERT: B 722 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7831 (mm) outliers start: 26 outliers final: 18 residues processed: 136 average time/residue: 0.1792 time to fit residues: 36.5396 Evaluate side-chains 132 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 121 optimal weight: 0.0060 chunk 71 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9945 Z= 0.200 Angle : 0.555 15.911 13588 Z= 0.265 Chirality : 0.042 0.214 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.807 87.870 1675 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.11 % Allowed : 19.40 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.18 (0.24), residues: 1307 helix: 0.83 (0.21), residues: 681 sheet: -1.24 (0.35), residues: 211 loop : -0.92 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.009 0.001 PHE A 226 TYR 0.019 0.001 TYR A 113 ARG 0.002 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7661 (mtp85) cc_final: 0.6830 (mtt90) REVERT: A 286 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7424 (mp) REVERT: A 650 ASN cc_start: 0.7554 (m-40) cc_final: 0.6825 (p0) REVERT: B 419 TRP cc_start: 0.7697 (m-10) cc_final: 0.7262 (m100) REVERT: B 722 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7870 (mm) outliers start: 26 outliers final: 19 residues processed: 140 average time/residue: 0.1779 time to fit residues: 37.2114 Evaluate side-chains 131 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 0.0670 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9945 Z= 0.214 Angle : 0.583 15.884 13588 Z= 0.274 Chirality : 0.043 0.212 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.573 86.737 1675 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.51 % Allowed : 20.36 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.24), residues: 1307 helix: 0.85 (0.21), residues: 681 sheet: -1.19 (0.36), residues: 200 loop : -0.91 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 419 HIS 0.003 0.001 HIS A 305 PHE 0.010 0.001 PHE A 226 TYR 0.021 0.001 TYR A 113 ARG 0.002 0.000 ARG A 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2614 Ramachandran restraints generated. 1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.7661 (mtp85) cc_final: 0.6828 (mtt90) REVERT: A 286 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7422 (mp) REVERT: A 419 TRP cc_start: 0.7934 (m100) cc_final: 0.7715 (m100) REVERT: A 650 ASN cc_start: 0.7532 (m-40) cc_final: 0.6833 (p0) REVERT: B 419 TRP cc_start: 0.7736 (m-10) cc_final: 0.7285 (m100) REVERT: B 722 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7888 (mm) outliers start: 21 outliers final: 19 residues processed: 129 average time/residue: 0.1862 time to fit residues: 35.9893 Evaluate side-chains 130 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 PHE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 MET Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 722 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.0010 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131817 restraints weight = 12494.090| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.42 r_work: 0.3304 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9945 Z= 0.198 Angle : 0.579 15.640 13588 Z= 0.270 Chirality : 0.042 0.203 1620 Planarity : 0.004 0.034 1691 Dihedral : 7.388 85.211 1675 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.75 % Allowed : 20.48 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.04 (0.24), residues: 1307 helix: 0.92 (0.21), residues: 681 sheet: -1.15 (0.36), residues: 202 loop : -0.85 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 419 HIS 0.003 0.001 HIS B 305 PHE 0.009 0.001 PHE A 226 TYR 0.019 0.001 TYR A 113 ARG 0.002 0.000 ARG A 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2215.17 seconds wall clock time: 40 minutes 48.03 seconds (2448.03 seconds total)