Starting phenix.real_space_refine on Wed Apr 10 16:36:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/04_2024/6u8a_20686_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/04_2024/6u8a_20686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/04_2024/6u8a_20686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/04_2024/6u8a_20686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/04_2024/6u8a_20686_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8a_20686/04_2024/6u8a_20686_updated.pdb" } resolution = 3.4 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: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13172 2.51 5 N 3324 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B GLU 708": "OE1" <-> "OE2" Residue "B GLU 709": "OE1" <-> "OE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C GLU 614": "OE1" <-> "OE2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ARG 563": "NH1" <-> "NH2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D GLU 614": "OE1" <-> "OE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D GLU 647": "OE1" <-> "OE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D ARG 706": "NH1" <-> "NH2" Residue "D GLU 708": "OE1" <-> "OE2" Residue "D GLU 709": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20032 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.18, per 1000 atoms: 0.51 Number of scatterers: 20032 At special positions: 0 Unit cell: (126.14, 126.14, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3420 8.00 N 3324 7.00 C 13172 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: 7.57 Conformation dependent library (CDL) restraints added in 3.3 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 53.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.576A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.856A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 378 through 412 removed outlier: 5.328A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 458 Processing helix chain 'A' and resid 472 through 491 removed outlier: 3.675A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 518 removed outlier: 4.291A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.706A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 603 removed outlier: 4.571A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 648 Processing helix chain 'A' and resid 656 through 671 Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.576A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.856A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 378 through 412 removed outlier: 5.328A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 458 Processing helix chain 'B' and resid 472 through 491 removed outlier: 3.674A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 518 removed outlier: 4.292A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 534 through 558 removed outlier: 3.706A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 603 removed outlier: 4.572A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 648 Processing helix chain 'B' and resid 656 through 671 Processing helix chain 'B' and resid 712 through 717 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.577A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.856A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 321 through 324 Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 378 through 412 removed outlier: 5.329A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 458 Processing helix chain 'C' and resid 472 through 491 removed outlier: 3.675A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 518 removed outlier: 4.292A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 534 through 558 removed outlier: 3.705A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 603 removed outlier: 4.571A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 648 Processing helix chain 'C' and resid 656 through 671 Processing helix chain 'C' and resid 712 through 717 Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.577A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 111 No H-bonds generated for 'chain 'D' and resid 109 through 111' Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 144 Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.856A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 321 through 324 Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 378 through 412 removed outlier: 5.328A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 458 Processing helix chain 'D' and resid 472 through 491 removed outlier: 3.675A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 518 removed outlier: 4.292A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ARG D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY D 518 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 534 through 558 removed outlier: 3.706A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 603 removed outlier: 4.571A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 648 Processing helix chain 'D' and resid 656 through 671 Processing helix chain 'D' and resid 712 through 717 Processing sheet with id= A, first strand: chain 'A' and resid 687 through 690 removed outlier: 6.026A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 687 through 690 removed outlier: 6.026A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 687 through 690 removed outlier: 6.026A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 687 through 690 removed outlier: 6.025A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) 908 hydrogen bonds defined for protein. 2688 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: 5.45 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6137 1.34 - 1.46: 5115 1.46 - 1.58: 9112 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 20544 Sorted by residual: bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T A1002 " pdb=" O02 P0T A1002 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T D1001 " pdb=" O02 P0T D1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C11 P0T A1001 " pdb=" O01 P0T A1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 20539 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.42: 380 105.42 - 112.58: 10583 112.58 - 119.75: 7226 119.75 - 126.92: 9376 126.92 - 134.09: 311 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N ILE D 529 " pdb=" CA ILE D 529 " pdb=" C ILE D 529 " ideal model delta sigma weight residual 111.91 108.09 3.82 8.90e-01 1.26e+00 1.84e+01 angle pdb=" N ILE B 529 " pdb=" CA ILE B 529 " pdb=" C ILE B 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.83e+01 angle pdb=" N ILE C 529 " pdb=" CA ILE C 529 " pdb=" C ILE C 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 122.80 -11.68 3.00e+00 1.11e-01 1.52e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 10837 19.27 - 38.53: 1023 38.53 - 57.80: 196 57.80 - 77.07: 32 77.07 - 96.33: 12 Dihedral angle restraints: 12100 sinusoidal: 4880 harmonic: 7220 Sorted by residual: dihedral pdb=" CA ASN C 655 " pdb=" C ASN C 655 " pdb=" N SER C 656 " pdb=" CA SER C 656 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 655 " pdb=" C ASN A 655 " pdb=" N SER A 656 " pdb=" CA SER A 656 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN B 655 " pdb=" C ASN B 655 " pdb=" N SER B 656 " pdb=" CA SER B 656 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1999 0.045 - 0.090: 861 0.090 - 0.135: 212 0.135 - 0.180: 68 0.180 - 0.225: 8 Chirality restraints: 3148 Sorted by residual: chirality pdb=" C03 P0T A1002 " pdb=" C04 P0T A1002 " pdb=" C05 P0T A1002 " pdb=" C10 P0T A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T C1001 " pdb=" C04 P0T C1001 " pdb=" C05 P0T C1001 " pdb=" C10 P0T C1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C05 P0T A1001 " pdb=" C10 P0T A1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3145 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 137 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO D 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6124 2.82 - 3.34: 18079 3.34 - 3.86: 33783 3.86 - 4.38: 38138 4.38 - 4.90: 66181 Nonbonded interactions: 162305 Sorted by model distance: nonbonded pdb=" O GLU C 90 " pdb=" OG1 THR C 93 " model vdw 2.296 2.440 nonbonded pdb=" O GLU D 90 " pdb=" OG1 THR D 93 " model vdw 2.296 2.440 nonbonded pdb=" O GLU A 90 " pdb=" OG1 THR A 93 " model vdw 2.297 2.440 nonbonded pdb=" O GLU B 90 " pdb=" OG1 THR B 93 " model vdw 2.297 2.440 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.302 2.520 ... (remaining 162300 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 32 through 719) selection = chain 'B' selection = (chain 'C' and resid 32 through 719) selection = (chain 'D' and resid 32 through 719) } 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: 0.010 Normalize map: mean=0, sd=1: 1.230 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: 0.020 Extract box with map and model: 6.370 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 51.060 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.008 0.065 20544 Z= 0.518 Angle : 0.966 11.681 27876 Z= 0.497 Chirality : 0.054 0.225 3148 Planarity : 0.007 0.067 3420 Dihedral : 15.898 96.335 7428 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.37 % Allowed : 8.94 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.94 (0.12), residues: 2428 helix: -2.38 (0.09), residues: 1460 sheet: -2.79 (0.43), residues: 92 loop : -2.72 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 333 HIS 0.006 0.002 HIS D 251 PHE 0.019 0.003 PHE B 161 TYR 0.013 0.002 TYR D 111 ARG 0.004 0.001 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 405 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7255 (mm) cc_final: 0.6674 (pp) REVERT: A 113 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6692 (mt-10) REVERT: A 173 GLU cc_start: 0.8400 (tp30) cc_final: 0.8198 (tp30) REVERT: A 541 LEU cc_start: 0.9104 (tp) cc_final: 0.8896 (tp) REVERT: B 255 MET cc_start: 0.8120 (mmm) cc_final: 0.7902 (mmm) REVERT: B 372 MET cc_start: 0.9125 (mtt) cc_final: 0.8903 (mtt) REVERT: B 383 GLN cc_start: 0.7898 (tp40) cc_final: 0.7604 (tt0) REVERT: B 404 MET cc_start: 0.8670 (mmp) cc_final: 0.8460 (mmt) REVERT: B 541 LEU cc_start: 0.9052 (tp) cc_final: 0.8787 (tp) REVERT: B 640 MET cc_start: 0.8412 (ttp) cc_final: 0.8069 (ttp) REVERT: C 113 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7058 (mt-10) REVERT: C 235 GLN cc_start: 0.7661 (mt0) cc_final: 0.7435 (mt0) REVERT: C 255 MET cc_start: 0.8176 (mmm) cc_final: 0.7930 (mmt) REVERT: C 464 TRP cc_start: 0.6065 (m100) cc_final: 0.5829 (m100) REVERT: D 113 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7088 (mt-10) REVERT: D 255 MET cc_start: 0.8169 (mmm) cc_final: 0.7959 (mmt) REVERT: D 305 GLU cc_start: 0.7603 (tt0) cc_final: 0.7064 (mt-10) REVERT: D 464 TRP cc_start: 0.6079 (m100) cc_final: 0.5860 (m100) REVERT: D 473 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7529 (mp0) REVERT: D 528 MET cc_start: 0.8073 (ttt) cc_final: 0.7569 (ttt) REVERT: D 536 ASP cc_start: 0.7392 (t70) cc_final: 0.7190 (t0) outliers start: 8 outliers final: 0 residues processed: 405 average time/residue: 0.3083 time to fit residues: 193.1132 Evaluate side-chains 270 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 191 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 186 ASN A 263 ASN A 316 GLN A 487 GLN A 530 GLN B 163 GLN B 186 ASN B 263 ASN B 316 GLN B 383 GLN B 530 GLN C 186 ASN C 263 ASN C 316 GLN C 530 GLN D 186 ASN D 263 ASN D 316 GLN D 487 GLN D 530 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20544 Z= 0.277 Angle : 0.581 7.978 27876 Z= 0.289 Chirality : 0.038 0.185 3148 Planarity : 0.005 0.066 3420 Dihedral : 7.510 64.230 2772 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.14 % Allowed : 14.85 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.76 (0.15), residues: 2428 helix: -0.42 (0.12), residues: 1484 sheet: -2.48 (0.44), residues: 92 loop : -2.23 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 715 HIS 0.004 0.001 HIS B 251 PHE 0.017 0.002 PHE B 405 TYR 0.012 0.001 TYR D 455 ARG 0.004 0.000 ARG B 706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 292 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6003 (p90) REVERT: A 92 LEU cc_start: 0.7286 (mm) cc_final: 0.6467 (pp) REVERT: A 113 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6867 (mt-10) REVERT: A 536 ASP cc_start: 0.7356 (t70) cc_final: 0.7104 (t0) REVERT: B 39 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.5947 (p90) REVERT: B 383 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7603 (tt0) REVERT: C 39 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.5534 (p90) REVERT: C 113 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6770 (mt-10) REVERT: C 464 TRP cc_start: 0.6159 (m100) cc_final: 0.5935 (m100) REVERT: D 39 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.5882 (p90) REVERT: D 113 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6899 (mt-10) REVERT: D 446 ILE cc_start: 0.9108 (tp) cc_final: 0.8855 (tp) REVERT: D 464 TRP cc_start: 0.6152 (m100) cc_final: 0.5922 (m100) REVERT: D 536 ASP cc_start: 0.7374 (t70) cc_final: 0.7093 (t0) outliers start: 46 outliers final: 19 residues processed: 327 average time/residue: 0.2941 time to fit residues: 152.9475 Evaluate side-chains 278 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 20544 Z= 0.307 Angle : 0.600 10.404 27876 Z= 0.290 Chirality : 0.039 0.162 3148 Planarity : 0.004 0.062 3420 Dihedral : 7.440 63.279 2772 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.61 % Allowed : 16.39 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.82 (0.16), residues: 2428 helix: 0.37 (0.13), residues: 1456 sheet: -2.32 (0.44), residues: 92 loop : -1.85 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 333 HIS 0.004 0.001 HIS D 313 PHE 0.018 0.002 PHE B 405 TYR 0.010 0.001 TYR B 629 ARG 0.003 0.000 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 260 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6235 (p90) REVERT: A 92 LEU cc_start: 0.7360 (mm) cc_final: 0.6553 (pp) REVERT: A 305 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7387 (tt0) REVERT: A 536 ASP cc_start: 0.7309 (t70) cc_final: 0.7059 (t0) REVERT: B 39 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.5808 (p90) REVERT: B 383 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7699 (tt0) REVERT: B 645 MET cc_start: 0.8245 (tmm) cc_final: 0.7624 (ttm) REVERT: C 39 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.5821 (p90) REVERT: C 113 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6776 (mt-10) REVERT: C 634 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7013 (m-80) REVERT: C 670 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7052 (tt0) REVERT: D 39 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6079 (p90) REVERT: D 113 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6758 (mt-10) REVERT: D 536 ASP cc_start: 0.7405 (t70) cc_final: 0.7127 (t0) REVERT: D 670 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7052 (tt0) outliers start: 56 outliers final: 31 residues processed: 297 average time/residue: 0.3106 time to fit residues: 148.8061 Evaluate side-chains 287 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 249 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 222 optimal weight: 0.0000 chunk 235 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 63 optimal weight: 0.0570 overall best weight: 0.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20544 Z= 0.132 Angle : 0.478 6.380 27876 Z= 0.235 Chirality : 0.035 0.147 3148 Planarity : 0.004 0.059 3420 Dihedral : 6.212 55.946 2772 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.72 % Allowed : 19.04 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.19 (0.17), residues: 2428 helix: 1.23 (0.14), residues: 1452 sheet: -1.72 (0.49), residues: 92 loop : -1.54 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 657 HIS 0.006 0.001 HIS B 313 PHE 0.018 0.001 PHE D 467 TYR 0.006 0.001 TYR C 629 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7232 (mm) cc_final: 0.6399 (pp) REVERT: A 269 HIS cc_start: 0.7453 (t70) cc_final: 0.7213 (t70) REVERT: A 332 GLU cc_start: 0.7614 (tt0) cc_final: 0.7379 (tt0) REVERT: A 536 ASP cc_start: 0.7344 (t70) cc_final: 0.7105 (t0) REVERT: A 634 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: A 647 GLU cc_start: 0.8184 (tt0) cc_final: 0.7833 (mt-10) REVERT: B 92 LEU cc_start: 0.7700 (mt) cc_final: 0.7253 (mt) REVERT: B 383 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7549 (tt0) REVERT: B 634 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: B 645 MET cc_start: 0.7991 (tmm) cc_final: 0.7160 (tmm) REVERT: C 113 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6527 (mt-10) REVERT: C 464 TRP cc_start: 0.6253 (m100) cc_final: 0.6047 (m100) REVERT: C 634 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: D 113 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6661 (mt-10) REVERT: D 255 MET cc_start: 0.8252 (tpp) cc_final: 0.7760 (mmt) REVERT: D 305 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7061 (tt0) REVERT: D 536 ASP cc_start: 0.7349 (t70) cc_final: 0.7074 (t0) REVERT: D 634 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.6996 (m-80) outliers start: 37 outliers final: 21 residues processed: 350 average time/residue: 0.2994 time to fit residues: 166.4089 Evaluate side-chains 311 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 286 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.0070 chunk 133 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 127 ASN B 163 GLN C 163 GLN C 487 GLN D 127 ASN D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20544 Z= 0.282 Angle : 0.566 9.980 27876 Z= 0.275 Chirality : 0.038 0.154 3148 Planarity : 0.004 0.052 3420 Dihedral : 7.031 59.094 2772 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.03 % Allowed : 19.04 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.22 (0.17), residues: 2428 helix: 1.25 (0.14), residues: 1448 sheet: -1.65 (0.50), residues: 92 loop : -1.53 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 333 HIS 0.006 0.001 HIS A 313 PHE 0.020 0.002 PHE B 405 TYR 0.010 0.001 TYR B 629 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 261 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.5913 (p90) REVERT: A 536 ASP cc_start: 0.7317 (t70) cc_final: 0.7066 (t0) REVERT: B 39 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.5807 (p90) REVERT: B 473 GLU cc_start: 0.7818 (mp0) cc_final: 0.7516 (mm-30) REVERT: B 634 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: B 645 MET cc_start: 0.8186 (tmm) cc_final: 0.7403 (tmm) REVERT: C 39 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.5764 (p90) REVERT: C 113 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6651 (mt-10) REVERT: C 473 GLU cc_start: 0.7815 (mp0) cc_final: 0.7507 (mm-30) REVERT: C 634 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: D 39 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.5937 (p90) REVERT: D 113 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6732 (mt-10) REVERT: D 473 GLU cc_start: 0.7808 (mp0) cc_final: 0.7490 (mm-30) REVERT: D 536 ASP cc_start: 0.7340 (t70) cc_final: 0.7106 (t0) REVERT: D 634 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6915 (m-80) outliers start: 65 outliers final: 36 residues processed: 308 average time/residue: 0.3048 time to fit residues: 148.2792 Evaluate side-chains 291 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 0.0980 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20544 Z= 0.201 Angle : 0.526 8.795 27876 Z= 0.256 Chirality : 0.037 0.135 3148 Planarity : 0.004 0.059 3420 Dihedral : 6.731 59.922 2772 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.61 % Allowed : 20.39 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.45 (0.17), residues: 2428 helix: 1.46 (0.14), residues: 1480 sheet: -1.64 (0.50), residues: 92 loop : -1.56 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 333 HIS 0.003 0.001 HIS D 251 PHE 0.020 0.001 PHE A 467 TYR 0.008 0.001 TYR A 629 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 ASP cc_start: 0.7283 (t70) cc_final: 0.7035 (t0) REVERT: A 634 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: B 634 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: C 113 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6574 (mt-10) REVERT: C 473 GLU cc_start: 0.7787 (mp0) cc_final: 0.7456 (mm-30) REVERT: C 634 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: D 113 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6652 (mt-10) REVERT: D 473 GLU cc_start: 0.7778 (mp0) cc_final: 0.7449 (mm-30) REVERT: D 536 ASP cc_start: 0.7289 (t70) cc_final: 0.7046 (t0) REVERT: D 634 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6940 (m-80) outliers start: 56 outliers final: 31 residues processed: 312 average time/residue: 0.2977 time to fit residues: 147.0275 Evaluate side-chains 286 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 TRP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 172 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 131 optimal weight: 0.0040 chunk 235 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20544 Z= 0.136 Angle : 0.514 12.170 27876 Z= 0.243 Chirality : 0.036 0.162 3148 Planarity : 0.003 0.050 3420 Dihedral : 6.265 59.845 2772 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.19 % Allowed : 21.46 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.94 (0.18), residues: 2428 helix: 1.85 (0.14), residues: 1452 sheet: -1.52 (0.52), residues: 92 loop : -1.26 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 715 HIS 0.007 0.001 HIS B 313 PHE 0.023 0.001 PHE A 467 TYR 0.008 0.001 TYR A 525 ARG 0.005 0.000 ARG C 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6017 (p90) REVERT: A 163 GLN cc_start: 0.7992 (tt0) cc_final: 0.7498 (tp40) REVERT: A 473 GLU cc_start: 0.7652 (mp0) cc_final: 0.7340 (mm-30) REVERT: A 536 ASP cc_start: 0.7347 (t70) cc_final: 0.7119 (t0) REVERT: A 634 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: A 647 GLU cc_start: 0.8206 (tt0) cc_final: 0.7880 (mt-10) REVERT: B 528 MET cc_start: 0.8192 (ptm) cc_final: 0.7902 (ttp) REVERT: B 634 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: B 645 MET cc_start: 0.7976 (tmm) cc_final: 0.7543 (ttm) REVERT: C 473 GLU cc_start: 0.7672 (mp0) cc_final: 0.7327 (mm-30) REVERT: C 634 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: D 39 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6039 (p90) REVERT: D 113 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6471 (mt-10) REVERT: D 473 GLU cc_start: 0.7674 (mp0) cc_final: 0.7314 (mm-30) REVERT: D 536 ASP cc_start: 0.7373 (t70) cc_final: 0.7121 (t0) REVERT: D 634 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6903 (m-80) outliers start: 47 outliers final: 31 residues processed: 324 average time/residue: 0.2939 time to fit residues: 151.4559 Evaluate side-chains 305 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 268 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN C 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20544 Z= 0.212 Angle : 0.547 10.980 27876 Z= 0.259 Chirality : 0.038 0.476 3148 Planarity : 0.003 0.047 3420 Dihedral : 6.524 58.506 2772 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.33 % Allowed : 21.97 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.76 (0.18), residues: 2428 helix: 1.69 (0.14), residues: 1480 sheet: -1.72 (0.50), residues: 92 loop : -1.40 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 715 HIS 0.006 0.001 HIS D 269 PHE 0.022 0.001 PHE A 467 TYR 0.009 0.001 TYR A 629 ARG 0.005 0.000 ARG D 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 265 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6093 (p90) REVERT: A 404 MET cc_start: 0.8542 (tpp) cc_final: 0.8242 (mmt) REVERT: A 473 GLU cc_start: 0.7718 (mp0) cc_final: 0.7419 (mm-30) REVERT: A 536 ASP cc_start: 0.7356 (t70) cc_final: 0.7075 (t0) REVERT: A 634 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: B 39 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.5656 (p90) REVERT: B 473 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 634 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6882 (m-80) REVERT: B 645 MET cc_start: 0.8140 (tmm) cc_final: 0.7720 (ttm) REVERT: C 39 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.5585 (p90) REVERT: C 404 MET cc_start: 0.8575 (tpp) cc_final: 0.8276 (mmt) REVERT: C 473 GLU cc_start: 0.7710 (mp0) cc_final: 0.7414 (mm-30) REVERT: C 545 LEU cc_start: 0.9338 (mm) cc_final: 0.9106 (mt) REVERT: C 634 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: D 39 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.5918 (p90) REVERT: D 404 MET cc_start: 0.8567 (tpp) cc_final: 0.8269 (mmt) REVERT: D 473 GLU cc_start: 0.7703 (mp0) cc_final: 0.7402 (mm-30) REVERT: D 536 ASP cc_start: 0.7427 (t70) cc_final: 0.7145 (t0) REVERT: D 634 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6859 (m-80) outliers start: 50 outliers final: 34 residues processed: 301 average time/residue: 0.3086 time to fit residues: 144.4576 Evaluate side-chains 297 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 255 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.4980 chunk 225 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20544 Z= 0.142 Angle : 0.517 14.549 27876 Z= 0.244 Chirality : 0.036 0.358 3148 Planarity : 0.003 0.048 3420 Dihedral : 6.204 58.893 2772 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.00 % Allowed : 22.21 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.07 (0.18), residues: 2428 helix: 1.94 (0.14), residues: 1456 sheet: -1.80 (0.49), residues: 92 loop : -1.15 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 715 HIS 0.005 0.001 HIS D 269 PHE 0.025 0.001 PHE A 467 TYR 0.008 0.001 TYR B 98 ARG 0.006 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 270 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.5994 (p90) REVERT: A 404 MET cc_start: 0.8633 (tpp) cc_final: 0.8403 (mmt) REVERT: A 473 GLU cc_start: 0.7650 (mp0) cc_final: 0.7367 (mm-30) REVERT: A 536 ASP cc_start: 0.7349 (t70) cc_final: 0.7110 (t0) REVERT: A 634 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6825 (m-80) REVERT: A 647 GLU cc_start: 0.8206 (tt0) cc_final: 0.7856 (mt-10) REVERT: B 39 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.5685 (p90) REVERT: B 92 LEU cc_start: 0.7677 (mt) cc_final: 0.7220 (mt) REVERT: B 473 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7375 (mm-30) REVERT: B 634 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: B 645 MET cc_start: 0.8015 (tmm) cc_final: 0.7583 (ttm) REVERT: C 404 MET cc_start: 0.8643 (tpp) cc_final: 0.8409 (mmt) REVERT: C 473 GLU cc_start: 0.7657 (mp0) cc_final: 0.7352 (mm-30) REVERT: C 634 TYR cc_start: 0.7707 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: D 39 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.5958 (p90) REVERT: D 111 TYR cc_start: 0.5414 (m-80) cc_final: 0.5045 (m-80) REVERT: D 404 MET cc_start: 0.8658 (tpp) cc_final: 0.8428 (mmt) REVERT: D 473 GLU cc_start: 0.7647 (mp0) cc_final: 0.7342 (mm-30) REVERT: D 536 ASP cc_start: 0.7411 (t70) cc_final: 0.7147 (t0) REVERT: D 634 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6856 (m-80) outliers start: 43 outliers final: 29 residues processed: 299 average time/residue: 0.3141 time to fit residues: 146.4504 Evaluate side-chains 289 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 719 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 161 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20544 Z= 0.149 Angle : 0.521 13.990 27876 Z= 0.245 Chirality : 0.036 0.343 3148 Planarity : 0.004 0.048 3420 Dihedral : 6.091 59.789 2772 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.00 % Allowed : 22.77 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.14 (0.18), residues: 2428 helix: 1.98 (0.14), residues: 1456 sheet: -1.78 (0.50), residues: 92 loop : -1.10 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 715 HIS 0.004 0.001 HIS C 313 PHE 0.025 0.001 PHE C 467 TYR 0.008 0.001 TYR A 98 ARG 0.006 0.000 ARG A 687 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 257 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.5919 (p90) REVERT: A 473 GLU cc_start: 0.7725 (mp0) cc_final: 0.7429 (mm-30) REVERT: A 536 ASP cc_start: 0.7336 (t70) cc_final: 0.7104 (t0) REVERT: A 634 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: A 647 GLU cc_start: 0.8212 (tt0) cc_final: 0.7865 (mt-10) REVERT: B 39 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.5699 (p90) REVERT: B 473 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 634 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6828 (m-80) REVERT: B 645 MET cc_start: 0.8023 (tmm) cc_final: 0.7311 (tmm) REVERT: C 634 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: D 39 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.5947 (p90) REVERT: D 536 ASP cc_start: 0.7426 (t70) cc_final: 0.7169 (t0) REVERT: D 634 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6834 (m-80) outliers start: 43 outliers final: 32 residues processed: 287 average time/residue: 0.3052 time to fit residues: 137.6628 Evaluate side-chains 282 residues out of total 2200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 243 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 223 TRP Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 470 SER Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 719 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.0670 chunk 206 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127489 restraints weight = 27208.144| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.79 r_work: 0.3294 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20544 Z= 0.142 Angle : 0.520 13.664 27876 Z= 0.247 Chirality : 0.036 0.331 3148 Planarity : 0.003 0.048 3420 Dihedral : 5.886 58.625 2772 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.77 % Allowed : 23.42 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.18), residues: 2428 helix: 2.02 (0.14), residues: 1456 sheet: -1.77 (0.49), residues: 92 loop : -1.07 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 715 HIS 0.004 0.001 HIS D 269 PHE 0.025 0.001 PHE A 467 TYR 0.007 0.001 TYR A 525 ARG 0.006 0.000 ARG D 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.23 seconds wall clock time: 77 minutes 28.54 seconds (4648.54 seconds total)