Starting phenix.real_space_refine on Mon Mar 18 10:13:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2s_23139/03_2024/7l2s_23139_updated.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 112 5.16 5 Na 1 4.78 5 C 13390 2.51 5 N 3327 2.21 5 O 3741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ASP 654": "OD1" <-> "OD2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 654": "OD1" <-> "OD2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20579 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5063 Classifications: {'peptide': 626} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 609} Chain: "A" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5057 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 609} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5063 Classifications: {'peptide': 626} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 609} Chain: "C" Number of atoms: 5083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5083 Classifications: {'peptide': 628} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 611} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'6IY': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {' NA': 1, '6IY': 1, 'XJ7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'6IY': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'6IY': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.82, per 1000 atoms: 0.53 Number of scatterers: 20579 At special positions: 0 Unit cell: (134.11, 134.11, 120.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 112 16.00 P 8 15.00 Na 1 11.00 O 3741 8.00 N 3327 7.00 C 13390 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: 8.05 Conformation dependent library (CDL) restraints added in 3.5 seconds 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 4 sheets defined 57.1% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 187 through 190 No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 453 removed outlier: 4.124A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 505 through 508 No H-bonds generated for 'chain 'D' and resid 505 through 508' Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.747A pdb=" N SER D 540 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.963A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 640 removed outlier: 4.011A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 686 Processing helix chain 'D' and resid 690 through 711 removed outlier: 3.586A pdb=" N SER D 711 " --> pdb=" O ASP D 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.986A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.893A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 4.269A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.919A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 4.015A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.594A pdb=" N GLU B 130 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 131 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU B 133 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 4.177A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 4.324A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.943A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 640 removed outlier: 4.045A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 686 Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.776A pdb=" N SER C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.854A pdb=" N LEU C 136 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 139 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 187 through 190 No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 4.100A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.292A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.925A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 4.039A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 686 removed outlier: 3.604A pdb=" N ILE C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 710 Processing sheet with id= A, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.604A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.677A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.633A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.649A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2622 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: 6.29 Time building geometry restraints manager: 8.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3232 1.30 - 1.43: 5716 1.43 - 1.56: 11879 1.56 - 1.69: 20 1.69 - 1.81: 180 Bond restraints: 21027 Sorted by residual: bond pdb=" C ARG A 500 " pdb=" O ARG A 500 " ideal model delta sigma weight residual 1.235 1.255 -0.020 4.70e-03 4.53e+04 1.85e+01 bond pdb=" O4 XJ7 D 801 " pdb=" P XJ7 D 801 " ideal model delta sigma weight residual 1.510 1.441 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O4 XJ7 C 902 " pdb=" P XJ7 C 902 " ideal model delta sigma weight residual 1.510 1.442 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O4 XJ7 A 801 " pdb=" P XJ7 A 801 " ideal model delta sigma weight residual 1.510 1.442 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O4 XJ7 B 801 " pdb=" P XJ7 B 801 " ideal model delta sigma weight residual 1.510 1.443 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 21022 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.24: 269 105.24 - 112.46: 10402 112.46 - 119.68: 7722 119.68 - 126.90: 9822 126.90 - 134.12: 203 Bond angle restraints: 28418 Sorted by residual: angle pdb=" O3 6IY B 802 " pdb=" P 6IY B 802 " pdb=" O4 6IY B 802 " ideal model delta sigma weight residual 123.06 100.53 22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" O3 6IY C 901 " pdb=" P 6IY C 901 " pdb=" O4 6IY C 901 " ideal model delta sigma weight residual 123.06 101.40 21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" O3 6IY A 802 " pdb=" P 6IY A 802 " pdb=" O4 6IY A 802 " ideal model delta sigma weight residual 123.06 101.41 21.65 3.00e+00 1.11e-01 5.21e+01 angle pdb=" O3 6IY D 802 " pdb=" P 6IY D 802 " pdb=" O4 6IY D 802 " ideal model delta sigma weight residual 123.06 101.55 21.51 3.00e+00 1.11e-01 5.14e+01 angle pdb=" N VAL D 728 " pdb=" CA VAL D 728 " pdb=" C VAL D 728 " ideal model delta sigma weight residual 111.62 106.08 5.54 7.90e-01 1.60e+00 4.92e+01 ... (remaining 28413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.19: 12306 30.19 - 60.38: 208 60.38 - 90.56: 42 90.56 - 120.75: 0 120.75 - 150.94: 2 Dihedral angle restraints: 12558 sinusoidal: 5175 harmonic: 7383 Sorted by residual: dihedral pdb=" CA ASP D 601 " pdb=" C ASP D 601 " pdb=" N GLY D 602 " pdb=" CA GLY D 602 " ideal model delta harmonic sigma weight residual 180.00 144.95 35.05 0 5.00e+00 4.00e-02 4.91e+01 dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -149.86 -30.14 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA VAL D 415 " pdb=" C VAL D 415 " pdb=" N GLU D 416 " pdb=" CA GLU D 416 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 12555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.015: 3198 1.015 - 2.031: 0 2.031 - 3.046: 0 3.046 - 4.062: 0 4.062 - 5.077: 8 Chirality restraints: 3206 Sorted by residual: chirality pdb=" C3 XJ7 A 801 " pdb=" C2 XJ7 A 801 " pdb=" C24 XJ7 A 801 " pdb=" O3 XJ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.58 -5.08 2.00e-01 2.50e+01 6.44e+02 chirality pdb=" C3 XJ7 D 801 " pdb=" C2 XJ7 D 801 " pdb=" C24 XJ7 D 801 " pdb=" O3 XJ7 D 801 " both_signs ideal model delta sigma weight residual False -2.50 2.55 -5.05 2.00e-01 2.50e+01 6.37e+02 chirality pdb=" C3 XJ7 C 902 " pdb=" C2 XJ7 C 902 " pdb=" C24 XJ7 C 902 " pdb=" O3 XJ7 C 902 " both_signs ideal model delta sigma weight residual False -2.50 2.54 -5.04 2.00e-01 2.50e+01 6.36e+02 ... (remaining 3203 not shown) Planarity restraints: 3523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 544 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C SER C 544 " 0.045 2.00e-02 2.50e+03 pdb=" O SER C 544 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 545 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 544 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C SER D 544 " -0.041 2.00e-02 2.50e+03 pdb=" O SER D 544 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU D 545 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 544 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C SER B 544 " 0.040 2.00e-02 2.50e+03 pdb=" O SER B 544 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 545 " -0.013 2.00e-02 2.50e+03 ... (remaining 3520 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 445 2.71 - 3.25: 20133 3.25 - 3.80: 30270 3.80 - 4.35: 40395 4.35 - 4.90: 68437 Nonbonded interactions: 159680 Sorted by model distance: nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.157 2.440 nonbonded pdb=" OG SER C 722 " pdb=" O CYS C 741 " model vdw 2.329 2.440 nonbonded pdb=" O LYS C 718 " pdb=" NH2 ARG C 721 " model vdw 2.350 2.520 nonbonded pdb=" OH TYR B 199 " pdb=" O ASP C 762 " model vdw 2.356 2.440 nonbonded pdb=" OG SER A 722 " pdb=" O CYS A 741 " model vdw 2.359 2.440 ... (remaining 159675 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 114 through 762) selection = (chain 'B' and (resid 114 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 762)) selection = (chain 'C' and (resid 114 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 762)) selection = (chain 'D' and (resid 114 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.060 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 53.720 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.120 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:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21027 Z= 0.429 Angle : 0.946 22.534 28418 Z= 0.483 Chirality : 0.255 5.077 3206 Planarity : 0.005 0.058 3523 Dihedral : 12.775 150.938 7802 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.04 % Favored : 93.92 % Rotamer: Outliers : 0.68 % Allowed : 1.31 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.35 (0.17), residues: 2498 helix: 1.37 (0.13), residues: 1447 sheet: 0.13 (0.51), residues: 76 loop : -1.54 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 697 HIS 0.005 0.001 HIS D 289 PHE 0.039 0.003 PHE A 135 TYR 0.019 0.003 TYR A 627 ARG 0.006 0.001 ARG A 721 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 411 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 263 ILE cc_start: 0.8711 (mt) cc_final: 0.8466 (mt) REVERT: D 267 LEU cc_start: 0.9159 (mt) cc_final: 0.8798 (mp) REVERT: D 322 THR cc_start: 0.9079 (p) cc_final: 0.8766 (t) REVERT: A 273 GLN cc_start: 0.7862 (tp40) cc_final: 0.7575 (tp40) REVERT: A 322 THR cc_start: 0.9044 (p) cc_final: 0.8816 (t) REVERT: A 324 LYS cc_start: 0.8605 (mttt) cc_final: 0.8321 (mmmt) REVERT: A 327 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 428 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7724 (mtp-110) REVERT: A 472 TYR cc_start: 0.8216 (m-80) cc_final: 0.7771 (m-80) REVERT: B 199 TYR cc_start: 0.7761 (m-80) cc_final: 0.7429 (m-80) REVERT: B 323 LEU cc_start: 0.8722 (tp) cc_final: 0.8311 (tp) REVERT: B 343 SER cc_start: 0.8898 (m) cc_final: 0.8637 (m) REVERT: B 389 THR cc_start: 0.8559 (m) cc_final: 0.8283 (p) REVERT: B 466 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8628 (mttm) REVERT: C 273 GLN cc_start: 0.7973 (tp40) cc_final: 0.7565 (tt0) REVERT: C 722 SER cc_start: 0.6875 (t) cc_final: 0.6599 (m) REVERT: C 746 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7369 (tt0) outliers start: 15 outliers final: 3 residues processed: 422 average time/residue: 1.4765 time to fit residues: 693.7325 Evaluate side-chains 277 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 274 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain C residue 162 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21027 Z= 0.148 Angle : 0.519 8.284 28418 Z= 0.273 Chirality : 0.042 0.523 3206 Planarity : 0.004 0.050 3523 Dihedral : 11.230 130.522 3013 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.16 % Allowed : 8.46 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.98 (0.17), residues: 2498 helix: 2.02 (0.13), residues: 1439 sheet: 0.42 (0.51), residues: 76 loop : -1.50 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 272 HIS 0.004 0.001 HIS B 378 PHE 0.017 0.001 PHE A 135 TYR 0.009 0.001 TYR C 565 ARG 0.007 0.000 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 291 time to evaluate : 2.061 Fit side-chains revert: symmetry clash REVERT: D 214 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7940 (tpt) REVERT: D 322 THR cc_start: 0.9081 (p) cc_final: 0.8819 (t) REVERT: A 213 ASN cc_start: 0.8252 (t0) cc_final: 0.7425 (t0) REVERT: A 273 GLN cc_start: 0.7721 (tp40) cc_final: 0.7321 (tp40) REVERT: A 303 LYS cc_start: 0.8304 (tppt) cc_final: 0.8013 (tttp) REVERT: A 322 THR cc_start: 0.9057 (p) cc_final: 0.8854 (t) REVERT: A 428 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7422 (mtp-110) REVERT: A 472 TYR cc_start: 0.8149 (m-80) cc_final: 0.7780 (m-80) REVERT: A 496 PHE cc_start: 0.8215 (t80) cc_final: 0.7380 (m-80) REVERT: A 500 ARG cc_start: 0.8357 (mmt180) cc_final: 0.8145 (mmt90) REVERT: A 743 ARG cc_start: 0.8502 (ttm110) cc_final: 0.8172 (ttp-170) REVERT: B 210 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: B 323 LEU cc_start: 0.8827 (tp) cc_final: 0.8605 (tp) REVERT: B 343 SER cc_start: 0.8773 (m) cc_final: 0.8506 (m) REVERT: B 553 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8785 (mp) REVERT: B 575 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7983 (mtt180) REVERT: C 213 ASN cc_start: 0.8019 (t0) cc_final: 0.7792 (t0) REVERT: C 273 GLN cc_start: 0.7872 (tp40) cc_final: 0.7409 (tt0) REVERT: C 746 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7317 (tt0) outliers start: 48 outliers final: 16 residues processed: 316 average time/residue: 1.4174 time to fit residues: 502.8883 Evaluate side-chains 280 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 260 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 493 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN B 164 ASN B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 21027 Z= 0.432 Angle : 0.641 10.577 28418 Z= 0.337 Chirality : 0.047 0.474 3206 Planarity : 0.005 0.052 3523 Dihedral : 11.037 125.596 3010 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.59 % Rotamer: Outliers : 2.52 % Allowed : 9.59 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.66 (0.17), residues: 2498 helix: 1.80 (0.13), residues: 1446 sheet: 0.46 (0.51), residues: 76 loop : -1.76 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 697 HIS 0.006 0.001 HIS B 378 PHE 0.027 0.002 PHE C 304 TYR 0.020 0.002 TYR C 627 ARG 0.004 0.000 ARG B 739 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 254 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 214 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7983 (tpt) REVERT: D 273 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: A 213 ASN cc_start: 0.8369 (t0) cc_final: 0.7511 (t0) REVERT: A 363 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7638 (ttt-90) REVERT: A 428 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7541 (mtp-110) REVERT: A 472 TYR cc_start: 0.8345 (m-80) cc_final: 0.7909 (m-80) REVERT: A 496 PHE cc_start: 0.8258 (t80) cc_final: 0.7436 (m-80) REVERT: A 648 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: A 716 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5360 (mpp) REVERT: A 720 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: B 343 SER cc_start: 0.8865 (m) cc_final: 0.8615 (m) REVERT: B 553 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8788 (mp) REVERT: C 211 ARG cc_start: 0.8677 (mmm160) cc_final: 0.8389 (mmm-85) REVERT: C 273 GLN cc_start: 0.7943 (tp40) cc_final: 0.7506 (tt0) REVERT: C 432 ARG cc_start: 0.7601 (mmt180) cc_final: 0.7230 (mmt90) REVERT: C 746 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7400 (tt0) outliers start: 56 outliers final: 31 residues processed: 290 average time/residue: 1.4187 time to fit residues: 462.0090 Evaluate side-chains 276 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 494 GLN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21027 Z= 0.139 Angle : 0.495 8.406 28418 Z= 0.260 Chirality : 0.039 0.372 3206 Planarity : 0.004 0.052 3523 Dihedral : 10.194 111.044 3010 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.58 % Allowed : 11.26 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.10 (0.17), residues: 2498 helix: 2.23 (0.14), residues: 1433 sheet: 0.78 (0.51), residues: 76 loop : -1.67 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 740 HIS 0.004 0.001 HIS B 378 PHE 0.014 0.001 PHE A 135 TYR 0.009 0.001 TYR C 199 ARG 0.003 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 261 time to evaluate : 2.358 Fit side-chains revert: symmetry clash REVERT: D 322 THR cc_start: 0.9050 (p) cc_final: 0.8785 (t) REVERT: D 363 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7751 (ttt-90) REVERT: D 432 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7296 (mtm180) REVERT: D 575 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8109 (mtt180) REVERT: A 323 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 332 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8887 (mtmm) REVERT: A 363 ARG cc_start: 0.7952 (ttp-110) cc_final: 0.7685 (ttt-90) REVERT: A 428 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7311 (mtp-110) REVERT: A 472 TYR cc_start: 0.8264 (m-80) cc_final: 0.7818 (m-80) REVERT: B 323 LEU cc_start: 0.8868 (tp) cc_final: 0.8621 (tp) REVERT: B 343 SER cc_start: 0.8731 (m) cc_final: 0.8469 (m) REVERT: B 464 LYS cc_start: 0.8460 (mmtm) cc_final: 0.7933 (mmtm) REVERT: B 575 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7826 (mtt180) REVERT: C 211 ARG cc_start: 0.8647 (mmm160) cc_final: 0.8182 (mmm-85) REVERT: C 213 ASN cc_start: 0.8101 (t0) cc_final: 0.7369 (t0) REVERT: C 273 GLN cc_start: 0.7913 (tp40) cc_final: 0.7518 (tt0) REVERT: C 746 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7293 (tt0) REVERT: C 762 ASP cc_start: 0.7098 (p0) cc_final: 0.6812 (p0) outliers start: 35 outliers final: 17 residues processed: 282 average time/residue: 1.4079 time to fit residues: 444.5660 Evaluate side-chains 266 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 215 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21027 Z= 0.370 Angle : 0.601 10.162 28418 Z= 0.315 Chirality : 0.045 0.430 3206 Planarity : 0.004 0.053 3523 Dihedral : 10.597 112.920 3010 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.20 % Favored : 93.76 % Rotamer: Outliers : 2.07 % Allowed : 11.17 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.78 (0.17), residues: 2498 helix: 1.91 (0.13), residues: 1453 sheet: 0.74 (0.51), residues: 76 loop : -1.78 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 697 HIS 0.006 0.001 HIS B 378 PHE 0.025 0.002 PHE C 304 TYR 0.017 0.002 TYR C 627 ARG 0.008 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 211 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8147 (mmm160) REVERT: D 267 LEU cc_start: 0.9002 (mt) cc_final: 0.8662 (mp) REVERT: D 322 THR cc_start: 0.9044 (p) cc_final: 0.8765 (t) REVERT: D 363 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7764 (ttt-90) REVERT: D 504 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7965 (tptm) REVERT: A 213 ASN cc_start: 0.8279 (t0) cc_final: 0.7570 (t0) REVERT: A 428 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7482 (mtp-110) REVERT: A 472 TYR cc_start: 0.8345 (m-80) cc_final: 0.7971 (m-80) REVERT: A 496 PHE cc_start: 0.8113 (t80) cc_final: 0.7296 (m-80) REVERT: A 720 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: B 343 SER cc_start: 0.8860 (m) cc_final: 0.8617 (m) REVERT: C 211 ARG cc_start: 0.8655 (mmm160) cc_final: 0.8328 (mmm-85) REVERT: C 213 ASN cc_start: 0.8271 (t0) cc_final: 0.7465 (t0) REVERT: C 273 GLN cc_start: 0.7964 (tp40) cc_final: 0.7572 (tt0) REVERT: C 432 ARG cc_start: 0.7540 (mmt180) cc_final: 0.7162 (mmt90) REVERT: C 746 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7377 (tt0) REVERT: C 762 ASP cc_start: 0.7148 (p0) cc_final: 0.6874 (p0) outliers start: 46 outliers final: 24 residues processed: 285 average time/residue: 1.3586 time to fit residues: 436.4804 Evaluate side-chains 266 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 240 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 199 optimal weight: 0.0050 chunk 111 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 0.0570 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN D 727 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21027 Z= 0.127 Angle : 0.493 10.130 28418 Z= 0.257 Chirality : 0.039 0.351 3206 Planarity : 0.003 0.054 3523 Dihedral : 9.762 111.183 3010 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.62 % Allowed : 12.07 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.17 (0.17), residues: 2498 helix: 2.32 (0.14), residues: 1437 sheet: 0.97 (0.51), residues: 76 loop : -1.72 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 740 HIS 0.004 0.001 HIS B 378 PHE 0.012 0.001 PHE A 304 TYR 0.008 0.001 TYR C 565 ARG 0.006 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 267 LEU cc_start: 0.8984 (mt) cc_final: 0.8644 (mp) REVERT: D 322 THR cc_start: 0.9032 (p) cc_final: 0.8782 (t) REVERT: D 363 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7612 (ttt-90) REVERT: D 432 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7202 (mtm180) REVERT: D 575 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (mtt180) REVERT: D 746 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: A 213 ASN cc_start: 0.8196 (t0) cc_final: 0.7560 (t0) REVERT: A 323 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 332 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8907 (mtmm) REVERT: A 363 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7726 (ttt-90) REVERT: A 500 ARG cc_start: 0.8252 (mmt180) cc_final: 0.8044 (mmt90) REVERT: B 327 GLU cc_start: 0.8451 (mp0) cc_final: 0.8199 (pm20) REVERT: B 343 SER cc_start: 0.8649 (m) cc_final: 0.8392 (m) REVERT: B 361 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7515 (tp30) REVERT: B 575 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7754 (mtt180) REVERT: C 211 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8355 (mmm-85) REVERT: C 273 GLN cc_start: 0.7914 (tp40) cc_final: 0.7553 (tt0) REVERT: C 746 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7338 (tt0) REVERT: C 762 ASP cc_start: 0.7121 (p0) cc_final: 0.6764 (p0) outliers start: 36 outliers final: 16 residues processed: 282 average time/residue: 1.3831 time to fit residues: 437.8854 Evaluate side-chains 267 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 493 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN A 467 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21027 Z= 0.200 Angle : 0.524 13.095 28418 Z= 0.272 Chirality : 0.040 0.368 3206 Planarity : 0.004 0.054 3523 Dihedral : 9.887 112.534 3010 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.53 % Allowed : 12.38 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.12 (0.17), residues: 2498 helix: 2.23 (0.14), residues: 1437 sheet: 0.93 (0.52), residues: 76 loop : -1.65 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 697 HIS 0.005 0.001 HIS B 378 PHE 0.032 0.001 PHE A 496 TYR 0.012 0.001 TYR A 584 ARG 0.006 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 267 LEU cc_start: 0.8945 (mt) cc_final: 0.8606 (mp) REVERT: D 322 THR cc_start: 0.9031 (p) cc_final: 0.8779 (t) REVERT: D 363 ARG cc_start: 0.7961 (mtp-110) cc_final: 0.7613 (ttt-90) REVERT: A 210 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: A 323 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 332 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8921 (mtmm) REVERT: A 363 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7711 (ttt-90) REVERT: A 428 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7390 (mpt-90) REVERT: A 500 ARG cc_start: 0.8249 (mmt180) cc_final: 0.8020 (mmt90) REVERT: B 273 GLN cc_start: 0.8038 (tt0) cc_final: 0.7448 (tp40) REVERT: B 343 SER cc_start: 0.8770 (m) cc_final: 0.8512 (m) REVERT: B 361 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7562 (tp30) REVERT: B 575 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7879 (mtt180) REVERT: C 211 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8368 (mmm-85) REVERT: C 273 GLN cc_start: 0.7918 (tp40) cc_final: 0.7556 (tt0) REVERT: C 746 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7342 (tt0) REVERT: C 762 ASP cc_start: 0.7142 (p0) cc_final: 0.6810 (p0) outliers start: 34 outliers final: 21 residues processed: 276 average time/residue: 1.4029 time to fit residues: 436.3795 Evaluate side-chains 271 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 162 optimal weight: 0.0060 chunk 118 optimal weight: 0.7980 chunk 22 optimal weight: 0.0070 chunk 187 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.4814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN A 467 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21027 Z= 0.113 Angle : 0.483 12.941 28418 Z= 0.250 Chirality : 0.038 0.337 3206 Planarity : 0.003 0.055 3523 Dihedral : 9.397 111.284 3010 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.17 % Allowed : 12.70 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.29 (0.18), residues: 2498 helix: 2.37 (0.14), residues: 1444 sheet: 1.04 (0.51), residues: 76 loop : -1.63 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 740 HIS 0.004 0.000 HIS B 378 PHE 0.011 0.001 PHE A 304 TYR 0.007 0.001 TYR B 194 ARG 0.006 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 2.221 Fit side-chains revert: symmetry clash REVERT: D 267 LEU cc_start: 0.8952 (mt) cc_final: 0.8618 (mp) REVERT: D 322 THR cc_start: 0.9051 (p) cc_final: 0.8817 (t) REVERT: D 363 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7620 (ttt-90) REVERT: D 432 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7193 (mtm180) REVERT: D 575 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7977 (mtt180) REVERT: A 213 ASN cc_start: 0.8080 (t0) cc_final: 0.7387 (t0) REVERT: A 323 LEU cc_start: 0.8938 (tp) cc_final: 0.8479 (tp) REVERT: A 332 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8859 (mtmm) REVERT: A 363 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7678 (ttt-90) REVERT: A 428 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7343 (mpt-90) REVERT: A 496 PHE cc_start: 0.7797 (t80) cc_final: 0.6890 (m-10) REVERT: A 500 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7977 (mmt90) REVERT: B 162 MET cc_start: 0.8058 (mmm) cc_final: 0.7722 (mmt) REVERT: B 273 GLN cc_start: 0.8074 (tt0) cc_final: 0.7472 (tp40) REVERT: B 343 SER cc_start: 0.8597 (m) cc_final: 0.8336 (m) REVERT: B 361 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7529 (tp30) REVERT: B 464 LYS cc_start: 0.8343 (mmtm) cc_final: 0.7891 (mptt) REVERT: B 575 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7646 (mtt180) REVERT: C 273 GLN cc_start: 0.7878 (tp40) cc_final: 0.7531 (tt0) REVERT: C 762 ASP cc_start: 0.7187 (p0) cc_final: 0.6783 (p0) outliers start: 26 outliers final: 16 residues processed: 283 average time/residue: 1.3682 time to fit residues: 435.9220 Evaluate side-chains 273 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 253 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 762 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 393 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21027 Z= 0.161 Angle : 0.517 16.396 28418 Z= 0.264 Chirality : 0.039 0.354 3206 Planarity : 0.004 0.055 3523 Dihedral : 9.464 112.401 3010 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.99 % Allowed : 13.33 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.24 (0.17), residues: 2498 helix: 2.31 (0.14), residues: 1440 sheet: 1.08 (0.52), residues: 76 loop : -1.60 (0.20), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.005 0.001 HIS B 378 PHE 0.016 0.001 PHE A 304 TYR 0.010 0.001 TYR A 584 ARG 0.006 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 250 time to evaluate : 2.386 Fit side-chains revert: symmetry clash REVERT: D 267 LEU cc_start: 0.8967 (mt) cc_final: 0.8637 (mp) REVERT: D 322 THR cc_start: 0.9047 (p) cc_final: 0.8809 (t) REVERT: D 363 ARG cc_start: 0.7959 (mtp-110) cc_final: 0.7647 (ttt-90) REVERT: D 575 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8092 (mtt180) REVERT: A 210 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: A 213 ASN cc_start: 0.8100 (t0) cc_final: 0.7396 (t0) REVERT: A 323 LEU cc_start: 0.8937 (tp) cc_final: 0.8453 (tp) REVERT: A 363 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7579 (ttt-90) REVERT: A 428 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7345 (mpt-90) REVERT: A 496 PHE cc_start: 0.7813 (t80) cc_final: 0.6935 (m-10) REVERT: A 500 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7968 (mmt90) REVERT: B 273 GLN cc_start: 0.8088 (tt0) cc_final: 0.7499 (tp40) REVERT: B 327 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: B 343 SER cc_start: 0.8756 (m) cc_final: 0.8494 (m) REVERT: B 361 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7525 (tp30) REVERT: B 464 LYS cc_start: 0.8343 (mmtm) cc_final: 0.7903 (mptt) REVERT: B 575 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7780 (mtt180) REVERT: C 211 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8385 (mmm-85) REVERT: C 273 GLN cc_start: 0.7895 (tp40) cc_final: 0.7553 (tt0) REVERT: C 762 ASP cc_start: 0.7189 (p0) cc_final: 0.6867 (p0) outliers start: 22 outliers final: 15 residues processed: 266 average time/residue: 1.4082 time to fit residues: 420.5775 Evaluate side-chains 269 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.3980 chunk 143 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN A 467 ASN C 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21027 Z= 0.131 Angle : 0.512 14.381 28418 Z= 0.260 Chirality : 0.039 0.343 3206 Planarity : 0.003 0.055 3523 Dihedral : 9.269 111.844 3010 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.95 % Allowed : 13.51 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.30 (0.18), residues: 2498 helix: 2.37 (0.14), residues: 1436 sheet: 1.19 (0.53), residues: 76 loop : -1.59 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 740 HIS 0.004 0.001 HIS B 378 PHE 0.013 0.001 PHE A 304 TYR 0.007 0.001 TYR A 584 ARG 0.007 0.000 ARG C 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4996 Ramachandran restraints generated. 2498 Oldfield, 0 Emsley, 2498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 260 time to evaluate : 2.397 Fit side-chains revert: symmetry clash REVERT: D 213 ASN cc_start: 0.8035 (t0) cc_final: 0.7609 (t0) REVERT: D 267 LEU cc_start: 0.8952 (mt) cc_final: 0.8615 (mp) REVERT: D 322 THR cc_start: 0.9043 (p) cc_final: 0.8815 (t) REVERT: D 363 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7626 (ttt-90) REVERT: D 575 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7911 (mtt180) REVERT: A 210 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: A 213 ASN cc_start: 0.8102 (t0) cc_final: 0.7403 (t0) REVERT: A 323 LEU cc_start: 0.8923 (tp) cc_final: 0.8447 (tp) REVERT: A 363 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7561 (ttt-90) REVERT: A 428 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7320 (mpt-90) REVERT: A 496 PHE cc_start: 0.7745 (t80) cc_final: 0.6874 (m-10) REVERT: B 343 SER cc_start: 0.8664 (m) cc_final: 0.8408 (m) REVERT: B 361 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7490 (tp30) REVERT: B 464 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7877 (mptt) REVERT: B 575 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7679 (mtt180) REVERT: C 273 GLN cc_start: 0.7874 (tp40) cc_final: 0.7550 (tt0) REVERT: C 746 GLU cc_start: 0.7380 (tt0) cc_final: 0.7109 (tt0) REVERT: C 762 ASP cc_start: 0.7357 (p0) cc_final: 0.6992 (p0) outliers start: 21 outliers final: 15 residues processed: 275 average time/residue: 1.3973 time to fit residues: 432.4781 Evaluate side-chains 276 residues out of total 2222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 575 ARG Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 762 ASP Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 575 ARG Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 393 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.087298 restraints weight = 25184.668| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.32 r_work: 0.2707 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21027 Z= 0.237 Angle : 0.570 14.043 28418 Z= 0.292 Chirality : 0.041 0.378 3206 Planarity : 0.004 0.055 3523 Dihedral : 9.698 113.245 3010 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.31 % Allowed : 13.37 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.09 (0.17), residues: 2498 helix: 2.19 (0.14), residues: 1431 sheet: 1.05 (0.53), residues: 76 loop : -1.63 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 740 HIS 0.005 0.001 HIS B 378 PHE 0.020 0.002 PHE C 304 TYR 0.013 0.001 TYR A 584 ARG 0.004 0.000 ARG C 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8185.98 seconds wall clock time: 145 minutes 33.07 seconds (8733.07 seconds total)