Starting phenix.real_space_refine (version: dev) on Sat Feb 18 16:39:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/02_2023/7rxb_24727_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/02_2023/7rxb_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_24727/02_2023/7rxb_24727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/02_2023/7rxb_24727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/02_2023/7rxb_24727_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxb_24727/02_2023/7rxb_24727_updated.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 83 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: 83 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: 5.49, per 1000 atoms: 0.65 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: 3.23 Conformation dependent library (CDL) restraints added in 1.4 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: 1.01 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: 2.23 Time building geometry restraints manager: 3.45 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 - 23.44: 4715 23.44 - 46.88: 243 46.88 - 70.33: 32 70.33 - 93.77: 0 93.77 - 117.21: 4 Dihedral angle restraints: 4994 sinusoidal: 1764 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 4991 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 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. 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: 1.620 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: 4.300 Check model and map are aligned: 0.130 Process input model: 25.250 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 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 : 14.602 117.209 2886 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 % 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 *********************** 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 : 0.976 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1729 time to fit residues: 20.8423 Evaluate side-chains 62 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4656 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8980 overall best weight: 0.4814 ------------------------------------------------------------------------------- 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: 0.8810 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 8718 Z= 0.119 Angle : 0.496 7.925 11890 Z= 0.263 Chirality : 0.038 0.145 1400 Planarity : 0.005 0.053 1438 Dihedral : 11.701 113.917 1286 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.25 % 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: -2.66 (0.24), residues: 1060 helix: -1.50 (0.18), residues: 696 sheet: -0.44 (0.58), residues: 44 loop : -2.18 (0.32), residues: 320 *********************** 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 80 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.115 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.1783 time to fit residues: 21.3445 Evaluate side-chains 67 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3812 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8899 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 8718 Z= 0.433 Angle : 0.639 7.750 11890 Z= 0.336 Chirality : 0.045 0.138 1400 Planarity : 0.006 0.053 1438 Dihedral : 11.606 118.910 1286 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.76 % 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: -2.55 (0.25), residues: 1060 helix: -1.34 (0.19), residues: 726 sheet: 0.67 (0.68), residues: 44 loop : -2.59 (0.33), residues: 290 *********************** 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 66 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 1.053 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 64 average time/residue: 0.1408 time to fit residues: 15.1933 Evaluate side-chains 64 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0735 time to fit residues: 1.8557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 0.0170 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 51 optimal weight: 0.0670 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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: 0.8787 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 8718 Z= 0.109 Angle : 0.459 7.381 11890 Z= 0.243 Chirality : 0.038 0.143 1400 Planarity : 0.004 0.044 1438 Dihedral : 10.208 106.712 1286 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.43 % Favored : 95.38 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.26), residues: 1060 helix: -0.55 (0.20), residues: 708 sheet: 0.67 (0.66), residues: 44 loop : -1.96 (0.35), residues: 308 *********************** 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 76 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.906 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.1470 time to fit residues: 18.3146 Evaluate side-chains 65 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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: 0.8898 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 8718 Z= 0.470 Angle : 0.641 7.588 11890 Z= 0.335 Chirality : 0.046 0.147 1400 Planarity : 0.005 0.045 1438 Dihedral : 10.969 116.635 1286 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.01 % 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: -1.97 (0.26), residues: 1060 helix: -0.94 (0.20), residues: 724 sheet: 1.15 (0.73), residues: 44 loop : -2.29 (0.35), residues: 292 *********************** 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 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.008 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.1433 time to fit residues: 15.5825 Evaluate side-chains 67 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0945 time to fit residues: 2.4741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.8818 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 8718 Z= 0.127 Angle : 0.469 7.318 11890 Z= 0.249 Chirality : 0.038 0.134 1400 Planarity : 0.004 0.044 1438 Dihedral : 10.017 108.904 1286 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.76 % 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: -1.19 (0.27), residues: 1060 helix: -0.37 (0.21), residues: 716 sheet: 1.21 (0.74), residues: 44 loop : -1.86 (0.36), residues: 300 *********************** 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 71 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.024 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 71 average time/residue: 0.1384 time to fit residues: 16.3314 Evaluate side-chains 66 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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: 0.8882 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 8718 Z= 0.372 Angle : 0.589 7.501 11890 Z= 0.308 Chirality : 0.044 0.131 1400 Planarity : 0.005 0.043 1438 Dihedral : 10.312 113.979 1286 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.88 % 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: -1.48 (0.26), residues: 1060 helix: -0.57 (0.20), residues: 716 sheet: 1.28 (0.74), residues: 44 loop : -2.06 (0.35), residues: 300 *********************** 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 70 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.038 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 67 average time/residue: 0.1411 time to fit residues: 15.8570 Evaluate side-chains 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0788 time to fit residues: 2.2450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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: 0.8808 moved from start: 0.1534 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= 0.137 Angle : 0.469 7.341 11890 Z= 0.246 Chirality : 0.038 0.130 1400 Planarity : 0.004 0.043 1438 Dihedral : 9.247 104.850 1286 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.13 % 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: -0.87 (0.27), residues: 1060 helix: -0.14 (0.21), residues: 716 sheet: 1.31 (0.76), residues: 44 loop : -1.73 (0.37), residues: 300 *********************** 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 69 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 1.018 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.1572 time to fit residues: 17.5760 Evaluate side-chains 67 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0779 time to fit residues: 1.3970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.8484 ------------------------------------------------------------------------------- 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: 0.8852 moved from start: 0.1414 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= 0.248 Angle : 0.523 7.404 11890 Z= 0.274 Chirality : 0.041 0.126 1400 Planarity : 0.004 0.042 1438 Dihedral : 9.351 106.068 1286 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 1060 helix: -0.18 (0.20), residues: 714 sheet: 1.43 (0.78), residues: 44 loop : -1.83 (0.36), residues: 302 *********************** 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 70 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.011 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.1459 time to fit residues: 16.9014 Evaluate side-chains 67 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0799 time to fit residues: 1.6778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 0.0000 chunk 66 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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: 0.8798 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 8718 Z= 0.125 Angle : 0.459 7.318 11890 Z= 0.241 Chirality : 0.038 0.130 1400 Planarity : 0.004 0.042 1438 Dihedral : 8.822 98.453 1286 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.00 % 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: -0.50 (0.27), residues: 1060 helix: 0.17 (0.21), residues: 714 sheet: 1.56 (0.80), residues: 44 loop : -1.66 (0.37), residues: 302 ********************** 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 66 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.065 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1440 time to fit residues: 15.7435 Evaluate side-chains 66 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.0060 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.118292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.088680 restraints weight = 10203.302| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.58 r_work: 0.2730 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 8718 Z= 0.123 Angle : 0.455 7.330 11890 Z= 0.238 Chirality : 0.038 0.131 1400 Planarity : 0.004 0.041 1438 Dihedral : 8.537 91.658 1286 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.00 % 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: -0.20 (0.28), residues: 1060 helix: 0.38 (0.21), residues: 712 sheet: 1.60 (0.80), residues: 44 loop : -1.48 (0.37), residues: 304 =============================================================================== Job complete usr+sys time: 1702.02 seconds wall clock time: 31 minutes 55.56 seconds (1915.56 seconds total)