Starting phenix.real_space_refine on Sun Feb 18 01:16:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz6_24084/02_2024/7mz6_24084_updated.pdb" } resolution = 2.91 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 13280 2.51 5 N 3288 2.21 5 O 3688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 557": "NH1" <-> "NH2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 654": "OD1" <-> "OD2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20377 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5016 Classifications: {'peptide': 619} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 602} Chain: "D" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5016 Classifications: {'peptide': 619} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 602} Chain: "B" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5016 Classifications: {'peptide': 619} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 602} Chain: "C" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5016 Classifications: {'peptide': 619} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 602} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6IY': 2, 'XJ7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "C" 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} Time building chain proxies: 11.47, per 1000 atoms: 0.56 Number of scatterers: 20377 At special positions: 0 Unit cell: (135.942, 135.942, 119.262, 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 3688 8.00 N 3288 7.00 C 13280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.06 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: 8.03 Conformation dependent library (CDL) restraints added in 3.3 seconds 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 57.1% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 157 through 162 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 268 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 453 removed outlier: 5.260A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 4.048A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 4.065A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 4.088A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 690 through 711 Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 127 through 139 removed outlier: 4.728A pdb=" N SER D 131 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 133 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Proline residue: D 134 - end of helix removed outlier: 3.658A pdb=" N ARG D 138 " --> pdb=" O PHE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 162 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 268 Processing helix chain 'D' and resid 287 through 294 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: 5.354A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.203A 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: 3.689A pdb=" N SER D 540 " --> pdb=" O TYR D 537 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.887A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.168A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 removed outlier: 3.515A pdb=" N LYS D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 711 Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 157 through 162 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 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 268 Processing helix chain 'B' and resid 287 through 294 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 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 453 removed outlier: 5.278A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) 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: 4.048A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.924A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 4.044A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 711 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 139 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 268 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 453 removed outlier: 5.286A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) 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: 3.620A pdb=" N SER C 540 " --> pdb=" O TYR C 537 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.917A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 4.013A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.796A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.972A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.992A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.565A 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: 3.753A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2691 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: 6.17 Time building geometry restraints manager: 8.64 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: 3184 1.30 - 1.43: 5800 1.43 - 1.56: 11648 1.56 - 1.69: 16 1.69 - 1.82: 180 Bond restraints: 20828 Sorted by residual: bond pdb=" O4 XJ7 C 801 " pdb=" P XJ7 C 801 " ideal model delta sigma weight residual 1.510 1.434 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" O4 XJ7 B 801 " pdb=" P XJ7 B 801 " ideal model delta sigma weight residual 1.510 1.439 0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" O4 XJ7 D 801 " pdb=" P XJ7 D 801 " ideal model delta sigma weight residual 1.510 1.439 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C13 6IY C 802 " pdb=" O6 6IY C 802 " ideal model delta sigma weight residual 1.333 1.404 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O5 XJ7 C 801 " pdb=" P XJ7 C 801 " ideal model delta sigma weight residual 1.510 1.439 0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 20823 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.17: 223 104.17 - 111.63: 9482 111.63 - 119.09: 7402 119.09 - 126.55: 10807 126.55 - 134.01: 230 Bond angle restraints: 28144 Sorted by residual: angle pdb=" O3 6IY D 802 " pdb=" P 6IY D 802 " pdb=" O4 6IY D 802 " ideal model delta sigma weight residual 123.06 100.59 22.47 3.00e+00 1.11e-01 5.61e+01 angle pdb=" O3 6IY A 803 " pdb=" P 6IY A 803 " pdb=" O4 6IY A 803 " ideal model delta sigma weight residual 123.06 100.69 22.37 3.00e+00 1.11e-01 5.56e+01 angle pdb=" O3 6IY A 802 " pdb=" P 6IY A 802 " pdb=" O4 6IY A 802 " ideal model delta sigma weight residual 123.06 101.13 21.93 3.00e+00 1.11e-01 5.35e+01 angle pdb=" O3 6IY C 802 " pdb=" P 6IY C 802 " pdb=" O4 6IY C 802 " ideal model delta sigma weight residual 123.06 101.46 21.60 3.00e+00 1.11e-01 5.18e+01 angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 109.81 99.83 9.98 1.53e+00 4.27e-01 4.25e+01 ... (remaining 28139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.72: 11846 20.72 - 41.43: 443 41.43 - 62.15: 115 62.15 - 82.86: 24 82.86 - 103.58: 11 Dihedral angle restraints: 12439 sinusoidal: 5135 harmonic: 7304 Sorted by residual: 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 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL C 415 " pdb=" C VAL C 415 " pdb=" N GLU C 416 " pdb=" CA GLU C 416 " ideal model delta harmonic sigma weight residual 180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+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 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 12436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 3160 1.032 - 2.063: 0 2.063 - 3.095: 0 3.095 - 4.127: 0 4.127 - 5.158: 8 Chirality restraints: 3168 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 2.66 -5.16 2.00e-01 2.50e+01 6.65e+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 2.64 -5.14 2.00e-01 2.50e+01 6.60e+02 chirality pdb=" C3 XJ7 B 801 " pdb=" C2 XJ7 B 801 " pdb=" C24 XJ7 B 801 " pdb=" O3 XJ7 B 801 " both_signs ideal model delta sigma weight residual False -2.50 2.63 -5.14 2.00e-01 2.50e+01 6.59e+02 ... (remaining 3165 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 548 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C GLY A 548 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY A 548 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP A 549 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 543 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C PHE B 543 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE B 543 " -0.016 2.00e-02 2.50e+03 pdb=" N SER B 544 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 543 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C PHE D 543 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE D 543 " 0.015 2.00e-02 2.50e+03 pdb=" N SER D 544 " 0.014 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 260 2.65 - 3.21: 19850 3.21 - 3.77: 31549 3.77 - 4.34: 44693 4.34 - 4.90: 73536 Nonbonded interactions: 169888 Sorted by model distance: nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.085 2.440 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.086 2.440 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.087 2.440 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.172 2.440 nonbonded pdb=" O PHE D 135 " pdb=" OG SER D 139 " model vdw 2.207 2.440 ... (remaining 169883 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 111 through 752 or resid 801)) selection = chain 'B' selection = (chain 'C' and (resid 111 through 752 or resid 801)) selection = (chain 'D' and (resid 111 through 752 or resid 801)) } 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: 6.140 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: 0.000 Extract box with map and model: 7.490 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 54.150 Find NCS groups from input model: 1.600 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 20828 Z= 0.607 Angle : 0.913 22.471 28144 Z= 0.461 Chirality : 0.258 5.158 3168 Planarity : 0.004 0.041 3480 Dihedral : 12.792 103.581 7732 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.51 % Favored : 94.25 % Rotamer: Outliers : 0.77 % Allowed : 1.37 % Favored : 97.86 % 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: 0.24 (0.17), residues: 2468 helix: 0.85 (0.12), residues: 1576 sheet: -1.66 (0.54), residues: 76 loop : -0.89 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 549 HIS 0.007 0.001 HIS B 358 PHE 0.027 0.003 PHE A 304 TYR 0.020 0.002 TYR A 627 ARG 0.005 0.001 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 514 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7972 (mp10) cc_final: 0.7613 (mp10) REVERT: A 234 ASP cc_start: 0.8132 (m-30) cc_final: 0.7915 (m-30) REVERT: A 293 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8387 (mm-30) REVERT: A 307 SER cc_start: 0.8997 (t) cc_final: 0.8688 (p) REVERT: A 324 LYS cc_start: 0.8511 (mttt) cc_final: 0.8213 (mttp) REVERT: A 378 HIS cc_start: 0.8416 (p-80) cc_final: 0.8080 (p90) REVERT: A 438 PHE cc_start: 0.8785 (t80) cc_final: 0.8552 (t80) REVERT: A 561 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8015 (mp10) REVERT: D 162 MET cc_start: 0.8382 (mmm) cc_final: 0.8093 (mtp) REVERT: D 471 ASP cc_start: 0.7876 (m-30) cc_final: 0.7577 (m-30) REVERT: D 479 ILE cc_start: 0.9416 (mt) cc_final: 0.9199 (mm) REVERT: D 496 PHE cc_start: 0.7931 (t80) cc_final: 0.7498 (m-10) REVERT: D 523 MET cc_start: 0.8866 (tpp) cc_final: 0.8591 (tpt) REVERT: D 684 GLU cc_start: 0.7823 (tp30) cc_final: 0.7370 (tm-30) REVERT: B 199 TYR cc_start: 0.7980 (m-80) cc_final: 0.7649 (m-80) REVERT: B 311 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 465 LEU cc_start: 0.8706 (tp) cc_final: 0.7894 (tp) REVERT: B 504 LYS cc_start: 0.8533 (tttt) cc_final: 0.8284 (ttmt) REVERT: B 533 GLN cc_start: 0.8797 (mt0) cc_final: 0.8561 (mt0) REVERT: C 150 ASP cc_start: 0.7309 (t70) cc_final: 0.7069 (t0) REVERT: C 165 LEU cc_start: 0.9073 (mt) cc_final: 0.8685 (tp) REVERT: C 237 LYS cc_start: 0.7414 (mttt) cc_final: 0.7041 (mppt) REVERT: C 388 ASP cc_start: 0.8187 (t0) cc_final: 0.7971 (t0) REVERT: C 403 SER cc_start: 0.8529 (p) cc_final: 0.7358 (t) REVERT: C 506 LEU cc_start: 0.8760 (tp) cc_final: 0.8512 (tp) outliers start: 17 outliers final: 8 residues processed: 526 average time/residue: 1.3771 time to fit residues: 812.2095 Evaluate side-chains 353 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 345 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 722 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 722 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN D 301 ASN D 393 ASN D 498 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN B 498 GLN C 393 ASN C 419 ASN C 467 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20828 Z= 0.178 Angle : 0.567 10.314 28144 Z= 0.294 Chirality : 0.041 0.358 3168 Planarity : 0.004 0.052 3480 Dihedral : 10.863 89.764 2992 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.79 % Favored : 94.04 % Rotamer: Outliers : 2.46 % Allowed : 9.79 % Favored : 87.75 % 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: 0.69 (0.17), residues: 2468 helix: 1.29 (0.13), residues: 1576 sheet: -0.96 (0.58), residues: 76 loop : -0.99 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 697 HIS 0.002 0.001 HIS C 289 PHE 0.017 0.001 PHE A 304 TYR 0.015 0.001 TYR D 199 ARG 0.007 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 406 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7892 (mp10) cc_final: 0.7421 (mp10) REVERT: A 324 LYS cc_start: 0.8533 (mttt) cc_final: 0.7962 (mtmm) REVERT: A 327 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 378 HIS cc_start: 0.8111 (p-80) cc_final: 0.7664 (p90) REVERT: A 561 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7934 (mp10) REVERT: D 162 MET cc_start: 0.8328 (mmm) cc_final: 0.8046 (mtp) REVERT: D 361 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: D 471 ASP cc_start: 0.7789 (m-30) cc_final: 0.7506 (m-30) REVERT: D 496 PHE cc_start: 0.7916 (t80) cc_final: 0.7581 (m-10) REVERT: B 199 TYR cc_start: 0.7913 (m-80) cc_final: 0.7570 (m-80) REVERT: B 211 ARG cc_start: 0.8142 (mpt90) cc_final: 0.7693 (mmm-85) REVERT: B 214 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7849 (tpt) REVERT: B 307 SER cc_start: 0.9074 (t) cc_final: 0.8859 (m) REVERT: B 311 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 496 PHE cc_start: 0.8216 (t80) cc_final: 0.7841 (m-80) REVERT: B 504 LYS cc_start: 0.8603 (tttt) cc_final: 0.8323 (ttmt) REVERT: B 533 GLN cc_start: 0.8727 (mt0) cc_final: 0.8479 (mt0) REVERT: C 150 ASP cc_start: 0.7262 (t70) cc_final: 0.6993 (t0) REVERT: C 165 LEU cc_start: 0.9032 (mt) cc_final: 0.8744 (tp) REVERT: C 237 LYS cc_start: 0.7490 (mttt) cc_final: 0.7155 (mppt) REVERT: C 327 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8100 (mp0) REVERT: C 359 GLU cc_start: 0.7713 (pt0) cc_final: 0.7437 (pt0) REVERT: C 362 CYS cc_start: 0.8116 (m) cc_final: 0.7166 (m) outliers start: 54 outliers final: 21 residues processed: 430 average time/residue: 1.2772 time to fit residues: 622.3215 Evaluate side-chains 365 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 342 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 457 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 184 optimal weight: 0.0980 chunk 150 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN D 223 ASN D 498 GLN B 191 ASN B 213 ASN B 223 ASN B 393 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20828 Z= 0.173 Angle : 0.539 13.350 28144 Z= 0.279 Chirality : 0.039 0.254 3168 Planarity : 0.004 0.046 3480 Dihedral : 9.662 89.342 2988 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.51 % Favored : 94.29 % Rotamer: Outliers : 2.91 % Allowed : 11.52 % Favored : 85.56 % 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: 0.88 (0.17), residues: 2468 helix: 1.52 (0.13), residues: 1544 sheet: -0.51 (0.58), residues: 76 loop : -1.04 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.006 0.001 HIS B 378 PHE 0.017 0.001 PHE A 489 TYR 0.011 0.001 TYR D 199 ARG 0.008 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 370 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7701 (mp10) cc_final: 0.7332 (mp10) REVERT: A 324 LYS cc_start: 0.8591 (mttt) cc_final: 0.8000 (mtmm) REVERT: A 327 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 368 LYS cc_start: 0.8532 (tttt) cc_final: 0.8281 (tttp) REVERT: A 561 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8188 (mm-40) REVERT: D 162 MET cc_start: 0.8355 (mmm) cc_final: 0.7898 (mtp) REVERT: D 202 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: D 266 PHE cc_start: 0.8677 (t80) cc_final: 0.8412 (t80) REVERT: D 471 ASP cc_start: 0.7753 (m-30) cc_final: 0.7464 (m-30) REVERT: D 496 PHE cc_start: 0.7929 (t80) cc_final: 0.7693 (m-10) REVERT: B 199 TYR cc_start: 0.7792 (m-80) cc_final: 0.7489 (m-80) REVERT: B 211 ARG cc_start: 0.8016 (mpt90) cc_final: 0.7679 (mmm-85) REVERT: B 267 LEU cc_start: 0.9387 (mp) cc_final: 0.9184 (mp) REVERT: B 311 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7976 (mm-30) REVERT: B 360 PRO cc_start: 0.8387 (Cg_exo) cc_final: 0.7871 (Cg_endo) REVERT: B 460 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8034 (mt) REVERT: B 504 LYS cc_start: 0.8583 (tttt) cc_final: 0.8332 (ttmt) REVERT: B 533 GLN cc_start: 0.8698 (mt0) cc_final: 0.8411 (mt0) REVERT: C 150 ASP cc_start: 0.7225 (t70) cc_final: 0.6960 (t0) REVERT: C 165 LEU cc_start: 0.8994 (mt) cc_final: 0.8752 (tp) REVERT: C 237 LYS cc_start: 0.7527 (mttt) cc_final: 0.7210 (mppt) REVERT: C 327 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8098 (mp0) REVERT: C 359 GLU cc_start: 0.7666 (pt0) cc_final: 0.7398 (pt0) REVERT: C 363 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7407 (mmm-85) outliers start: 64 outliers final: 30 residues processed: 400 average time/residue: 1.2113 time to fit residues: 552.1467 Evaluate side-chains 374 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 342 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 553 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 235 optimal weight: 0.4980 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 0.3980 chunk 63 optimal weight: 20.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 378 HIS D 498 GLN B 213 ASN B 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20828 Z= 0.143 Angle : 0.518 13.631 28144 Z= 0.269 Chirality : 0.038 0.235 3168 Planarity : 0.004 0.047 3480 Dihedral : 9.023 89.775 2988 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 2.69 % Allowed : 12.70 % Favored : 84.61 % 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: 0.99 (0.17), residues: 2468 helix: 1.64 (0.13), residues: 1540 sheet: -0.28 (0.57), residues: 76 loop : -1.08 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 740 HIS 0.005 0.001 HIS A 378 PHE 0.015 0.001 PHE A 489 TYR 0.010 0.001 TYR C 199 ARG 0.007 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 364 time to evaluate : 2.345 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 188 GLN cc_start: 0.7729 (mp10) cc_final: 0.7387 (mp10) REVERT: A 324 LYS cc_start: 0.8586 (mttt) cc_final: 0.7973 (mtmm) REVERT: A 327 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7123 (mt-10) REVERT: A 368 LYS cc_start: 0.8496 (tttt) cc_final: 0.8290 (tttp) REVERT: A 561 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8149 (mm-40) REVERT: A 570 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: D 202 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: D 331 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7651 (mmt90) REVERT: D 471 ASP cc_start: 0.7723 (m-30) cc_final: 0.7415 (m-30) REVERT: D 496 PHE cc_start: 0.7913 (t80) cc_final: 0.7660 (m-10) REVERT: D 500 ARG cc_start: 0.7636 (mmm-85) cc_final: 0.7366 (mmm-85) REVERT: B 199 TYR cc_start: 0.7738 (m-80) cc_final: 0.7395 (m-80) REVERT: B 202 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: B 211 ARG cc_start: 0.8020 (mpt90) cc_final: 0.7528 (mmm-85) REVERT: B 360 PRO cc_start: 0.8406 (Cg_exo) cc_final: 0.8006 (Cg_endo) REVERT: B 384 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8626 (mp) REVERT: B 460 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7982 (mt) REVERT: B 496 PHE cc_start: 0.8208 (t80) cc_final: 0.7786 (m-80) REVERT: B 716 MET cc_start: 0.5735 (ttm) cc_final: 0.5436 (ttm) REVERT: C 150 ASP cc_start: 0.7191 (t70) cc_final: 0.6915 (t0) REVERT: C 165 LEU cc_start: 0.8969 (mt) cc_final: 0.8756 (tp) REVERT: C 237 LYS cc_start: 0.7538 (mttt) cc_final: 0.7222 (mppt) REVERT: C 318 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8544 (mttm) REVERT: C 359 GLU cc_start: 0.7587 (pt0) cc_final: 0.7376 (pt0) REVERT: C 494 GLN cc_start: 0.8338 (tt0) cc_final: 0.8126 (tt0) outliers start: 59 outliers final: 33 residues processed: 395 average time/residue: 1.2385 time to fit residues: 557.2517 Evaluate side-chains 387 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 348 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 736 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 211 optimal weight: 0.3980 chunk 59 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 551 ASN D 223 ASN D 498 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20828 Z= 0.201 Angle : 0.532 14.110 28144 Z= 0.275 Chirality : 0.038 0.238 3168 Planarity : 0.004 0.100 3480 Dihedral : 8.777 89.162 2988 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.59 % Favored : 94.25 % Rotamer: Outliers : 2.96 % Allowed : 14.12 % Favored : 82.92 % 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: 1.00 (0.17), residues: 2468 helix: 1.65 (0.13), residues: 1540 sheet: -0.16 (0.57), residues: 76 loop : -1.12 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 740 HIS 0.004 0.001 HIS B 378 PHE 0.031 0.001 PHE D 266 TYR 0.011 0.001 TYR A 487 ARG 0.008 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 365 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7714 (mp10) cc_final: 0.7368 (mp10) REVERT: A 211 ARG cc_start: 0.8637 (mmt180) cc_final: 0.8258 (mmt180) REVERT: A 324 LYS cc_start: 0.8535 (mttt) cc_final: 0.8105 (mtmm) REVERT: A 327 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7319 (mt-10) REVERT: A 368 LYS cc_start: 0.8551 (tttt) cc_final: 0.8321 (tttp) REVERT: A 560 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: A 561 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7921 (mp10) REVERT: D 202 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: D 361 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7418 (mm-30) REVERT: D 445 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.9099 (mmt) REVERT: D 471 ASP cc_start: 0.7771 (m-30) cc_final: 0.7461 (m-30) REVERT: D 496 PHE cc_start: 0.7911 (t80) cc_final: 0.7699 (m-10) REVERT: D 727 GLN cc_start: 0.6811 (tt0) cc_final: 0.6157 (tp40) REVERT: B 199 TYR cc_start: 0.7796 (m-80) cc_final: 0.7464 (m-80) REVERT: B 202 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: B 211 ARG cc_start: 0.7962 (mpt90) cc_final: 0.7602 (mmm-85) REVERT: B 214 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7765 (tpt) REVERT: B 384 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8737 (mp) REVERT: B 504 LYS cc_start: 0.8151 (tppt) cc_final: 0.7883 (ttmt) REVERT: B 716 MET cc_start: 0.5726 (ttm) cc_final: 0.5441 (ttm) REVERT: C 150 ASP cc_start: 0.7166 (t70) cc_final: 0.6904 (t0) REVERT: C 237 LYS cc_start: 0.7569 (mttt) cc_final: 0.7247 (mppt) REVERT: C 318 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8512 (mttm) REVERT: C 359 GLU cc_start: 0.7546 (pt0) cc_final: 0.7256 (pt0) REVERT: C 494 GLN cc_start: 0.8390 (tt0) cc_final: 0.8163 (tt0) outliers start: 65 outliers final: 33 residues processed: 398 average time/residue: 1.2474 time to fit residues: 564.7659 Evaluate side-chains 382 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 341 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 736 ASP 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: 3.9990 chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 0.6980 chunk 195 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS D 206 HIS D 498 GLN B 498 GLN ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20828 Z= 0.324 Angle : 0.599 15.479 28144 Z= 0.305 Chirality : 0.041 0.240 3168 Planarity : 0.004 0.069 3480 Dihedral : 8.901 89.904 2988 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Rotamer: Outliers : 2.96 % Allowed : 14.66 % Favored : 82.38 % 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: 0.85 (0.17), residues: 2468 helix: 1.51 (0.13), residues: 1544 sheet: -0.05 (0.57), residues: 76 loop : -1.16 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 549 HIS 0.005 0.001 HIS B 358 PHE 0.017 0.002 PHE D 266 TYR 0.011 0.001 TYR D 555 ARG 0.009 0.001 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 344 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7698 (mp10) cc_final: 0.7370 (mp10) REVERT: A 211 ARG cc_start: 0.8628 (mmt180) cc_final: 0.8380 (mmt180) REVERT: A 220 LEU cc_start: 0.8998 (mm) cc_final: 0.8774 (mm) REVERT: A 324 LYS cc_start: 0.8544 (mttt) cc_final: 0.7947 (mtmm) REVERT: A 327 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 560 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: A 721 ARG cc_start: 0.6043 (mmm160) cc_final: 0.5786 (mmm160) REVERT: D 202 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: D 384 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8753 (mp) REVERT: D 471 ASP cc_start: 0.7951 (m-30) cc_final: 0.7605 (m-30) REVERT: D 496 PHE cc_start: 0.7938 (t80) cc_final: 0.7713 (m-10) REVERT: B 202 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: B 211 ARG cc_start: 0.8075 (mpt90) cc_final: 0.7511 (mmm-85) REVERT: B 384 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8900 (mp) REVERT: B 504 LYS cc_start: 0.8195 (tppt) cc_final: 0.7928 (ttmt) REVERT: B 716 MET cc_start: 0.5825 (ttm) cc_final: 0.5551 (ttm) REVERT: C 150 ASP cc_start: 0.7166 (t70) cc_final: 0.6913 (t0) REVERT: C 237 LYS cc_start: 0.7520 (mttt) cc_final: 0.7179 (mppt) REVERT: C 403 SER cc_start: 0.7801 (p) cc_final: 0.7526 (t) REVERT: C 494 GLN cc_start: 0.8414 (tt0) cc_final: 0.8197 (tt0) REVERT: C 651 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7638 (mt-10) outliers start: 65 outliers final: 38 residues processed: 387 average time/residue: 1.2584 time to fit residues: 555.4455 Evaluate side-chains 377 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 333 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 578 CYS Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain D residue 655 PHE Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 736 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 0.0070 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 498 GLN B 498 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20828 Z= 0.143 Angle : 0.539 17.021 28144 Z= 0.274 Chirality : 0.038 0.232 3168 Planarity : 0.004 0.063 3480 Dihedral : 8.431 88.435 2988 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 2.28 % Allowed : 15.85 % Favored : 81.88 % 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: 1.03 (0.17), residues: 2468 helix: 1.69 (0.13), residues: 1524 sheet: 0.19 (0.57), residues: 76 loop : -1.12 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 740 HIS 0.004 0.001 HIS A 378 PHE 0.023 0.001 PHE A 489 TYR 0.016 0.001 TYR D 374 ARG 0.009 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 356 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 LYS cc_start: 0.8493 (mttt) cc_final: 0.7949 (mtmm) REVERT: A 327 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 529 LEU cc_start: 0.8724 (mp) cc_final: 0.8520 (mp) REVERT: A 560 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: D 202 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: D 361 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: D 445 MET cc_start: 0.9459 (mmt) cc_final: 0.9076 (mmt) REVERT: D 471 ASP cc_start: 0.7806 (m-30) cc_final: 0.7469 (m-30) REVERT: D 496 PHE cc_start: 0.7907 (t80) cc_final: 0.7694 (m-10) REVERT: D 506 LEU cc_start: 0.8526 (tt) cc_final: 0.8110 (tt) REVERT: B 202 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: B 211 ARG cc_start: 0.7996 (mpt90) cc_final: 0.7590 (mmm-85) REVERT: B 293 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8245 (mm-30) REVERT: B 384 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 460 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8064 (mt) REVERT: B 504 LYS cc_start: 0.8193 (tppt) cc_final: 0.7937 (ttmt) REVERT: C 150 ASP cc_start: 0.7050 (t70) cc_final: 0.6803 (t0) REVERT: C 237 LYS cc_start: 0.7554 (mttt) cc_final: 0.7236 (mppt) REVERT: C 494 GLN cc_start: 0.8410 (tt0) cc_final: 0.8197 (tt0) outliers start: 50 outliers final: 26 residues processed: 389 average time/residue: 1.2328 time to fit residues: 545.4608 Evaluate side-chains 376 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 344 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 736 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 378 HIS D 498 GLN C 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20828 Z= 0.151 Angle : 0.550 15.912 28144 Z= 0.277 Chirality : 0.038 0.410 3168 Planarity : 0.004 0.048 3480 Dihedral : 8.193 85.978 2988 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 2.09 % Allowed : 16.58 % Favored : 81.33 % 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: 1.00 (0.18), residues: 2468 helix: 1.67 (0.13), residues: 1536 sheet: 0.34 (0.58), residues: 76 loop : -1.19 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 740 HIS 0.004 0.001 HIS A 378 PHE 0.019 0.001 PHE A 438 TYR 0.014 0.001 TYR A 487 ARG 0.008 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 361 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.8970 (mm) cc_final: 0.8730 (mm) REVERT: A 226 ASP cc_start: 0.7952 (t0) cc_final: 0.7414 (t0) REVERT: A 293 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 324 LYS cc_start: 0.8495 (mttt) cc_final: 0.7959 (mtmm) REVERT: A 327 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 368 LYS cc_start: 0.8590 (tttt) cc_final: 0.8294 (tttp) REVERT: A 392 LYS cc_start: 0.8488 (pttt) cc_final: 0.8260 (pttp) REVERT: D 202 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: D 331 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7346 (mmt90) REVERT: D 420 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8023 (mtt90) REVERT: D 445 MET cc_start: 0.9450 (mmt) cc_final: 0.8907 (mmt) REVERT: D 471 ASP cc_start: 0.7834 (m-30) cc_final: 0.7497 (m-30) REVERT: B 199 TYR cc_start: 0.7733 (m-80) cc_final: 0.7438 (m-80) REVERT: B 211 ARG cc_start: 0.8035 (mpt90) cc_final: 0.7521 (mmm-85) REVERT: B 384 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8714 (mp) REVERT: B 460 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8014 (mt) REVERT: B 504 LYS cc_start: 0.8202 (tppt) cc_final: 0.7914 (ttmt) REVERT: B 710 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8369 (tppp) REVERT: B 716 MET cc_start: 0.5731 (ttm) cc_final: 0.5522 (ttm) REVERT: C 150 ASP cc_start: 0.7014 (t70) cc_final: 0.6766 (t0) REVERT: C 237 LYS cc_start: 0.7578 (mttt) cc_final: 0.7276 (mppt) REVERT: C 494 GLN cc_start: 0.8426 (tt0) cc_final: 0.8211 (tt0) REVERT: C 746 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6673 (tm-30) outliers start: 46 outliers final: 27 residues processed: 387 average time/residue: 1.2202 time to fit residues: 537.4543 Evaluate side-chains 375 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 345 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 736 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 219 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN D 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20828 Z= 0.177 Angle : 0.568 16.669 28144 Z= 0.283 Chirality : 0.039 0.391 3168 Planarity : 0.004 0.048 3480 Dihedral : 8.132 84.984 2988 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 2.05 % Allowed : 16.89 % Favored : 81.06 % 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: 0.99 (0.17), residues: 2468 helix: 1.66 (0.13), residues: 1536 sheet: 0.34 (0.58), residues: 76 loop : -1.19 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 740 HIS 0.002 0.001 HIS B 378 PHE 0.021 0.001 PHE A 489 TYR 0.011 0.001 TYR A 309 ARG 0.009 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 346 time to evaluate : 2.482 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 226 ASP cc_start: 0.7961 (t0) cc_final: 0.7441 (t0) REVERT: A 293 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 324 LYS cc_start: 0.8486 (mttt) cc_final: 0.7977 (mtmm) REVERT: A 327 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7162 (mt-10) REVERT: A 392 LYS cc_start: 0.8488 (pttt) cc_final: 0.8250 (pttp) REVERT: A 560 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: A 570 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: A 572 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8112 (mtp) REVERT: D 202 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: D 331 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7440 (mmt90) REVERT: D 420 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.8031 (mtt90) REVERT: D 445 MET cc_start: 0.9452 (mmt) cc_final: 0.8957 (mmt) REVERT: D 471 ASP cc_start: 0.7858 (m-30) cc_final: 0.7528 (m-30) REVERT: B 199 TYR cc_start: 0.7729 (m-80) cc_final: 0.7441 (m-80) REVERT: B 211 ARG cc_start: 0.8046 (mpt90) cc_final: 0.7448 (mmm-85) REVERT: B 384 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 504 LYS cc_start: 0.8180 (tppt) cc_final: 0.7902 (ttmt) REVERT: B 710 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8357 (tppp) REVERT: B 716 MET cc_start: 0.5757 (ttm) cc_final: 0.5543 (ttm) REVERT: C 150 ASP cc_start: 0.7009 (t70) cc_final: 0.6760 (t0) REVERT: C 237 LYS cc_start: 0.7584 (mttt) cc_final: 0.7280 (mppt) REVERT: C 494 GLN cc_start: 0.8439 (tt0) cc_final: 0.8234 (tt0) REVERT: C 746 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6570 (tm-30) outliers start: 45 outliers final: 28 residues processed: 373 average time/residue: 1.2413 time to fit residues: 528.9577 Evaluate side-chains 372 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 339 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 736 ASP 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: 0.5980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 193 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 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 191 ASN D 498 GLN ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20828 Z= 0.155 Angle : 0.587 16.255 28144 Z= 0.289 Chirality : 0.039 0.369 3168 Planarity : 0.004 0.048 3480 Dihedral : 8.023 83.499 2988 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 1.68 % Allowed : 17.53 % Favored : 80.78 % 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: 0.99 (0.17), residues: 2468 helix: 1.67 (0.13), residues: 1532 sheet: 0.38 (0.58), residues: 76 loop : -1.21 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 740 HIS 0.002 0.001 HIS B 378 PHE 0.023 0.001 PHE A 438 TYR 0.011 0.001 TYR A 309 ARG 0.009 0.000 ARG B 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 342 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7956 (t0) cc_final: 0.7444 (t0) REVERT: A 293 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8302 (mm-30) REVERT: A 324 LYS cc_start: 0.8477 (mttt) cc_final: 0.7976 (mtmm) REVERT: A 327 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7115 (mt-10) REVERT: A 392 LYS cc_start: 0.8510 (pttt) cc_final: 0.8278 (pttp) REVERT: D 202 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: D 331 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7437 (mmt90) REVERT: D 420 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.8068 (mtt90) REVERT: D 445 MET cc_start: 0.9444 (mmt) cc_final: 0.8906 (mmt) REVERT: D 471 ASP cc_start: 0.7846 (m-30) cc_final: 0.7526 (m-30) REVERT: B 199 TYR cc_start: 0.7720 (m-80) cc_final: 0.7434 (m-80) REVERT: B 211 ARG cc_start: 0.8026 (mpt90) cc_final: 0.7403 (mmm-85) REVERT: B 384 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 504 LYS cc_start: 0.8169 (tppt) cc_final: 0.7891 (ttmt) REVERT: C 150 ASP cc_start: 0.6941 (t70) cc_final: 0.6683 (t0) REVERT: C 237 LYS cc_start: 0.7591 (mttt) cc_final: 0.7298 (mppt) REVERT: C 494 GLN cc_start: 0.8457 (tt0) cc_final: 0.8250 (tt0) outliers start: 37 outliers final: 28 residues processed: 367 average time/residue: 1.2025 time to fit residues: 504.2539 Evaluate side-chains 365 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 335 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 654 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 736 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN D 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.098305 restraints weight = 27545.985| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.26 r_work: 0.2918 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20828 Z= 0.194 Angle : 0.594 15.970 28144 Z= 0.293 Chirality : 0.039 0.353 3168 Planarity : 0.004 0.054 3480 Dihedral : 8.009 82.297 2988 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % Rotamer: Outliers : 1.50 % Allowed : 17.85 % Favored : 80.65 % 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: 0.95 (0.17), residues: 2468 helix: 1.65 (0.13), residues: 1528 sheet: 0.36 (0.58), residues: 76 loop : -1.24 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 740 HIS 0.002 0.001 HIS C 289 PHE 0.057 0.001 PHE D 266 TYR 0.017 0.001 TYR A 487 ARG 0.009 0.000 ARG B 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8912.79 seconds wall clock time: 158 minutes 42.39 seconds (9522.39 seconds total)