Starting phenix.real_space_refine on Mon Mar 11 14:33:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/03_2024/7rxb_24727_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/03_2024/7rxb_24727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/03_2024/7rxb_24727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/03_2024/7rxb_24727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/03_2024/7rxb_24727_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/03_2024/7rxb_24727_updated.pdb" } resolution = 3.07 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= 0.005 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 32 5.16 5 C 5660 2.51 5 N 1382 2.21 5 O 1426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ASP 564": "OD1" <-> "OD2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8506 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4153 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 8 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 292 Chain: "B" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4153 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 21, 'TRANS': 526} Chain breaks: 8 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 29, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 292 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 5.00, per 1000 atoms: 0.59 Number of scatterers: 8506 At special positions: 0 Unit cell: (115.02, 74.124, 100.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 6 15.00 O 1426 8.00 N 1382 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 56.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.843A pdb=" N LYS A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.777A pdb=" N LEU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 175 through 197 removed outlier: 3.932A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.574A pdb=" N CYS A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.441A pdb=" N LEU A 281 " --> pdb=" O MET A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 310 removed outlier: 3.775A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 Proline residue: A 324 - end of helix removed outlier: 4.579A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 335 No H-bonds generated for 'chain 'A' and resid 332 through 335' Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 355 through 374 removed outlier: 3.553A pdb=" N LYS A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 379 No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 393 through 396 No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 493 through 502 removed outlier: 3.675A pdb=" N ARG A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 524 Processing helix chain 'A' and resid 532 through 542 removed outlier: 3.589A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 removed outlier: 4.586A pdb=" N ASP A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE A 548 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 550 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 586 removed outlier: 3.605A pdb=" N SER A 572 " --> pdb=" O TRP A 569 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 573 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY A 574 " --> pdb=" O ASP A 571 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 575 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 576 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 577 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A 579 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 581 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 591 No H-bonds generated for 'chain 'A' and resid 588 through 591' Processing helix chain 'A' and resid 607 through 629 removed outlier: 3.598A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 656 removed outlier: 3.797A pdb=" N ARG A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.843A pdb=" N ALA A 716 " --> pdb=" O TRP A 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 716' Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 69 through 86 removed outlier: 3.843A pdb=" N LYS B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.779A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 175 through 197 removed outlier: 3.932A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix Processing helix chain 'B' and resid 210 through 237 removed outlier: 3.573A pdb=" N CYS B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 221 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 4.440A pdb=" N LEU B 281 " --> pdb=" O MET B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 310 removed outlier: 3.775A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 329 Proline residue: B 324 - end of helix removed outlier: 4.580A pdb=" N LEU B 327 " --> pdb=" O PRO B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 No H-bonds generated for 'chain 'B' and resid 332 through 335' Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.554A pdb=" N LYS B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 379 No H-bonds generated for 'chain 'B' and resid 376 through 379' Processing helix chain 'B' and resid 393 through 396 No H-bonds generated for 'chain 'B' and resid 393 through 396' Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 493 through 502 removed outlier: 3.674A pdb=" N ARG B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 502 " --> pdb=" O ARG B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 532 through 542 removed outlier: 3.590A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 551 removed outlier: 4.587A pdb=" N ASP B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE B 548 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 549 " --> pdb=" O SER B 546 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 550 " --> pdb=" O ASP B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 586 removed outlier: 3.607A pdb=" N SER B 572 " --> pdb=" O TRP B 569 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 573 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY B 574 " --> pdb=" O ASP B 571 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 575 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 576 " --> pdb=" O LEU B 573 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 577 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL B 579 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 581 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 591 No H-bonds generated for 'chain 'B' and resid 588 through 591' Processing helix chain 'B' and resid 607 through 629 removed outlier: 3.599A pdb=" N PHE B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 656 removed outlier: 3.798A pdb=" N ARG B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 716 removed outlier: 3.844A pdb=" N ALA B 716 " --> pdb=" O TRP B 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 712 through 716' Processing sheet with id= A, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.974A pdb=" N ALA A 138 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASN A 23 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 136 " --> pdb=" O ASN A 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 48 through 54 removed outlier: 3.974A pdb=" N ALA B 138 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN B 23 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL B 136 " --> pdb=" O ASN B 23 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1002 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: 2.04 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1230 1.30 - 1.43: 2566 1.43 - 1.56: 4866 1.56 - 1.68: 12 1.68 - 1.81: 44 Bond restraints: 8718 Sorted by residual: bond pdb=" C1 PGW B1003 " pdb=" O01 PGW B1003 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 PGW A 802 " pdb=" O01 PGW A 802 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 PGW A 803 " pdb=" O01 PGW A 803 " ideal model delta sigma weight residual 1.332 1.417 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C1 PGW B1004 " pdb=" O01 PGW B1004 " ideal model delta sigma weight residual 1.332 1.417 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 PGW B1001 " pdb=" O01 PGW B1001 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.74e+01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.47: 339 107.47 - 114.53: 4972 114.53 - 121.59: 4785 121.59 - 128.65: 1701 128.65 - 135.71: 93 Bond angle restraints: 11890 Sorted by residual: angle pdb=" N ILE A 169 " pdb=" CA ILE A 169 " pdb=" C ILE A 169 " ideal model delta sigma weight residual 111.91 105.97 5.94 8.90e-01 1.26e+00 4.46e+01 angle pdb=" N ILE B 169 " pdb=" CA ILE B 169 " pdb=" C ILE B 169 " ideal model delta sigma weight residual 111.91 106.00 5.91 8.90e-01 1.26e+00 4.40e+01 angle pdb=" C LYS A 158 " pdb=" N THR A 159 " pdb=" CA THR A 159 " ideal model delta sigma weight residual 121.54 132.10 -10.56 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C LYS B 158 " pdb=" N THR B 159 " pdb=" CA THR B 159 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" O11 PGW B1001 " pdb=" P PGW B1001 " pdb=" O12 PGW B1001 " ideal model delta sigma weight residual 98.90 110.62 -11.72 3.00e+00 1.11e-01 1.53e+01 ... (remaining 11885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 4856 30.26 - 60.53: 160 60.53 - 90.79: 10 90.79 - 121.05: 4 121.05 - 151.32: 4 Dihedral angle restraints: 5034 sinusoidal: 1804 harmonic: 3230 Sorted by residual: dihedral pdb=" CA PHE B 399 " pdb=" C PHE B 399 " pdb=" N HIS B 400 " pdb=" CA HIS B 400 " ideal model delta harmonic sigma weight residual 180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 399 " pdb=" C PHE A 399 " pdb=" N HIS A 400 " pdb=" CA HIS A 400 " ideal model delta harmonic sigma weight residual -180.00 -156.74 -23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASN A 171 " pdb=" C ASN A 171 " pdb=" N THR A 172 " pdb=" CA THR A 172 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 663 0.037 - 0.073: 527 0.073 - 0.110: 130 0.110 - 0.146: 68 0.146 - 0.183: 12 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR B 159 " pdb=" N THR B 159 " pdb=" C THR B 159 " pdb=" CB THR B 159 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA THR A 159 " pdb=" N THR A 159 " pdb=" C THR A 159 " pdb=" CB THR A 159 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA SER A 526 " pdb=" N SER A 526 " pdb=" C SER A 526 " pdb=" CB SER A 526 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 ... (remaining 1397 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 422 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 423 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 422 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO A 423 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 376 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 377 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.040 5.00e-02 4.00e+02 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 3367 2.93 - 3.42: 7580 3.42 - 3.91: 12824 3.91 - 4.41: 14822 4.41 - 4.90: 25973 Nonbonded interactions: 64566 Sorted by model distance: nonbonded pdb=" O SER A 209 " pdb=" OG1 THR A 213 " model vdw 2.437 2.440 nonbonded pdb=" O SER B 209 " pdb=" OG1 THR B 213 " model vdw 2.437 2.440 nonbonded pdb=" O THR B 613 " pdb=" OG SER B 617 " model vdw 2.448 2.440 nonbonded pdb=" O THR A 613 " pdb=" OG SER A 617 " model vdw 2.448 2.440 nonbonded pdb=" O01 PGW B1002 " pdb=" O11 PGW B1002 " model vdw 2.452 2.432 ... (remaining 64561 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 11 through 717 or (resid 801 and (name C01 or name C02 or \ name C03 or name C19 or name O03 or name O04 or name O11 or name O12 or name O13 \ or name O14 or name P )) or (resid 802 and (name C01 or name C02 or name C03 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name O0 \ 3 or name O04)) or (resid 803 and (name C01 or name C02 or name C03 or name C1 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C3 or name C4 or name C5 or name C6 or name O01 or name O0 \ 2 or name O03 or name O04)) or resid 804)) selection = (chain 'B' and (resid 11 through 717 or (resid 1001 and (name C01 or name C02 or \ name C03 or name C19 or name O03 or name O04 or name O11 or name O12 or name O1 \ 3 or name O14 or name P )) or (resid 1002 and (name C01 or name C02 or name C03 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ O03 or name O04)) or resid 1003 or (resid 1004 and (name C01 or name C02 or name \ C03 or name C1 or name C19 or name C2 or name C20 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name O01 or name O02 or name O03 or name O04 or nam \ e O11 or name O12 or name O13 or name O14 or name P )))) } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.910 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.009 0.087 8718 Z= 0.604 Angle : 1.151 11.724 11890 Z= 0.569 Chirality : 0.055 0.183 1400 Planarity : 0.008 0.079 1438 Dihedral : 16.228 151.317 2926 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.18), residues: 1060 helix: -3.22 (0.13), residues: 710 sheet: -0.67 (0.61), residues: 44 loop : -3.09 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 227 HIS 0.008 0.002 HIS A 130 PHE 0.016 0.002 PHE A 140 TYR 0.014 0.002 TYR A 589 ARG 0.006 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.963 Fit side-chains REVERT: A 551 ILE cc_start: 0.8368 (tt) cc_final: 0.7892 (tp) REVERT: B 21 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8075 (ttp-170) REVERT: B 551 ILE cc_start: 0.8344 (tt) cc_final: 0.7954 (tt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1654 time to fit residues: 19.9389 Evaluate side-chains 64 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.0060 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 370 ASN A 518 GLN B 280 GLN B 370 ASN B 518 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8718 Z= 0.133 Angle : 0.503 7.918 11890 Z= 0.267 Chirality : 0.038 0.143 1400 Planarity : 0.005 0.054 1438 Dihedral : 14.999 123.778 1326 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.50 % Allowed : 6.68 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.24), residues: 1060 helix: -1.52 (0.18), residues: 698 sheet: -0.38 (0.59), residues: 44 loop : -2.17 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 202 HIS 0.003 0.001 HIS B 619 PHE 0.010 0.001 PHE A 140 TYR 0.009 0.001 TYR B 589 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.992 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.1581 time to fit residues: 18.7567 Evaluate side-chains 66 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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: 0.8490 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8718 Z= 0.266 Angle : 0.548 7.655 11890 Z= 0.288 Chirality : 0.041 0.123 1400 Planarity : 0.005 0.047 1438 Dihedral : 14.400 119.258 1326 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.25 % Allowed : 10.33 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.25), residues: 1060 helix: -1.12 (0.19), residues: 720 sheet: 0.45 (0.64), residues: 44 loop : -2.36 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 227 HIS 0.005 0.002 HIS B 619 PHE 0.009 0.001 PHE A 286 TYR 0.013 0.001 TYR B 589 ARG 0.002 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.966 Fit side-chains REVERT: A 551 ILE cc_start: 0.8388 (tt) cc_final: 0.7977 (tt) REVERT: B 551 ILE cc_start: 0.8398 (tt) cc_final: 0.7978 (tt) outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 0.1346 time to fit residues: 14.9278 Evaluate side-chains 67 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain B residue 163 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.8474 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8718 Z= 0.214 Angle : 0.512 7.479 11890 Z= 0.270 Chirality : 0.040 0.143 1400 Planarity : 0.004 0.044 1438 Dihedral : 13.590 113.233 1326 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.13 % Allowed : 10.58 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.26), residues: 1060 helix: -0.76 (0.20), residues: 720 sheet: 0.84 (0.70), residues: 44 loop : -2.07 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.004 0.001 HIS A 619 PHE 0.008 0.001 PHE A 286 TYR 0.010 0.001 TYR B 589 ARG 0.001 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.989 Fit side-chains REVERT: A 167 ASP cc_start: 0.8900 (m-30) cc_final: 0.8645 (m-30) REVERT: A 551 ILE cc_start: 0.8340 (tt) cc_final: 0.7912 (tt) REVERT: B 551 ILE cc_start: 0.8393 (tt) cc_final: 0.7978 (tt) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 0.1396 time to fit residues: 16.4373 Evaluate side-chains 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 509 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.8473 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8718 Z= 0.216 Angle : 0.513 7.531 11890 Z= 0.270 Chirality : 0.040 0.127 1400 Planarity : 0.004 0.042 1438 Dihedral : 13.150 109.967 1326 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.88 % Allowed : 10.58 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.26), residues: 1060 helix: -0.55 (0.20), residues: 720 sheet: 1.18 (0.74), residues: 44 loop : -1.95 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.004 0.001 HIS A 619 PHE 0.008 0.001 PHE A 286 TYR 0.010 0.001 TYR B 589 ARG 0.001 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.979 Fit side-chains REVERT: A 551 ILE cc_start: 0.8359 (tt) cc_final: 0.7945 (tt) REVERT: B 551 ILE cc_start: 0.8351 (tt) cc_final: 0.7918 (tt) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.1383 time to fit residues: 16.0937 Evaluate side-chains 68 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 509 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 34 optimal weight: 0.0070 chunk 54 optimal weight: 6.9990 overall best weight: 0.3826 ------------------------------------------------------------------------------- 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: 0.8392 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8718 Z= 0.105 Angle : 0.447 7.410 11890 Z= 0.234 Chirality : 0.037 0.133 1400 Planarity : 0.004 0.039 1438 Dihedral : 12.037 103.453 1326 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.38 % Allowed : 11.84 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 1060 helix: 0.00 (0.21), residues: 712 sheet: 1.21 (0.74), residues: 44 loop : -1.67 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.002 0.001 HIS A 619 PHE 0.007 0.001 PHE A 615 TYR 0.008 0.001 TYR B 180 ARG 0.001 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.996 Fit side-chains REVERT: B 71 LYS cc_start: 0.8285 (mttm) cc_final: 0.8025 (mttt) REVERT: B 551 ILE cc_start: 0.8267 (tt) cc_final: 0.7820 (tt) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 0.1692 time to fit residues: 20.5427 Evaluate side-chains 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 509 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8718 Z= 0.292 Angle : 0.536 7.494 11890 Z= 0.281 Chirality : 0.042 0.125 1400 Planarity : 0.004 0.038 1438 Dihedral : 12.344 107.643 1326 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.76 % Allowed : 11.59 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 1060 helix: -0.16 (0.20), residues: 714 sheet: 1.47 (0.77), residues: 44 loop : -1.88 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.006 0.002 HIS A 619 PHE 0.009 0.001 PHE A 616 TYR 0.011 0.001 TYR A 589 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.861 Fit side-chains REVERT: A 551 ILE cc_start: 0.8384 (tt) cc_final: 0.7966 (tt) REVERT: B 551 ILE cc_start: 0.8381 (tt) cc_final: 0.7962 (tt) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1424 time to fit residues: 15.9578 Evaluate side-chains 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 509 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8422 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8718 Z= 0.134 Angle : 0.463 7.398 11890 Z= 0.242 Chirality : 0.038 0.130 1400 Planarity : 0.004 0.037 1438 Dihedral : 11.583 102.954 1326 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.38 % Allowed : 12.72 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 1060 helix: 0.17 (0.21), residues: 712 sheet: 1.59 (0.78), residues: 44 loop : -1.63 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.003 0.001 HIS B 619 PHE 0.007 0.001 PHE A 615 TYR 0.008 0.001 TYR B 180 ARG 0.001 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.947 Fit side-chains REVERT: A 551 ILE cc_start: 0.8309 (tt) cc_final: 0.7878 (tt) REVERT: B 551 ILE cc_start: 0.8346 (tt) cc_final: 0.7925 (tt) outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.1415 time to fit residues: 16.2240 Evaluate side-chains 71 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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: 0.8490 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8718 Z= 0.310 Angle : 0.555 7.467 11890 Z= 0.290 Chirality : 0.042 0.128 1400 Planarity : 0.004 0.037 1438 Dihedral : 12.179 108.140 1326 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.01 % Allowed : 12.09 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.27), residues: 1060 helix: -0.15 (0.20), residues: 720 sheet: 1.68 (0.79), residues: 44 loop : -1.87 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.006 0.002 HIS A 619 PHE 0.010 0.001 PHE B 616 TYR 0.012 0.001 TYR A 589 ARG 0.002 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.023 Fit side-chains REVERT: A 551 ILE cc_start: 0.8391 (tt) cc_final: 0.7974 (tt) REVERT: B 551 ILE cc_start: 0.8379 (tt) cc_final: 0.7967 (tt) outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.1348 time to fit residues: 16.4674 Evaluate side-chains 76 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8464 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8718 Z= 0.204 Angle : 0.503 7.402 11890 Z= 0.264 Chirality : 0.040 0.127 1400 Planarity : 0.004 0.037 1438 Dihedral : 11.872 106.254 1326 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.50 % Allowed : 12.72 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 1060 helix: 0.00 (0.20), residues: 720 sheet: 1.69 (0.80), residues: 44 loop : -1.79 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.004 0.001 HIS A 619 PHE 0.007 0.001 PHE A 615 TYR 0.008 0.001 TYR B 180 ARG 0.001 0.000 ARG A 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.013 Fit side-chains REVERT: A 551 ILE cc_start: 0.8368 (tt) cc_final: 0.7949 (tt) REVERT: B 551 ILE cc_start: 0.8358 (tt) cc_final: 0.7938 (tt) outliers start: 4 outliers final: 4 residues processed: 69 average time/residue: 0.1422 time to fit residues: 16.1274 Evaluate side-chains 71 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.3199 r_free = 0.3199 target = 0.113322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.083729 restraints weight = 10375.953| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.57 r_work: 0.2660 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8718 Z= 0.242 Angle : 0.521 7.425 11890 Z= 0.273 Chirality : 0.041 0.126 1400 Planarity : 0.004 0.037 1438 Dihedral : 11.912 107.065 1326 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.76 % Allowed : 12.59 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 1060 helix: -0.02 (0.20), residues: 720 sheet: 1.68 (0.79), residues: 44 loop : -1.82 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.005 0.001 HIS A 619 PHE 0.008 0.001 PHE A 575 TYR 0.010 0.001 TYR A 589 ARG 0.001 0.000 ARG A 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.62 seconds wall clock time: 32 minutes 16.94 seconds (1936.94 seconds total)