Starting phenix.real_space_refine on Wed Feb 14 09:49:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojh_12951/02_2024/7ojh_12951_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojh_12951/02_2024/7ojh_12951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojh_12951/02_2024/7ojh_12951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojh_12951/02_2024/7ojh_12951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojh_12951/02_2024/7ojh_12951_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojh_12951/02_2024/7ojh_12951_updated.pdb" } resolution = 3.1 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= 0.005 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 58 5.16 5 C 5839 2.51 5 N 1471 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "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: 8999 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 18, 'TRANS': 550} Chain breaks: 3 Chain: "A" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4425 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 18, 'TRANS': 550} Chain breaks: 3 Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 90 Unusual residues: {'ATP': 1, 'CLR': 1, 'TTC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.04, per 1000 atoms: 0.56 Number of scatterers: 8999 At special positions: 0 Unit cell: (90.42, 95.7, 122.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 6 15.00 O 1625 8.00 N 1471 7.00 C 5839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS A 603 " distance=2.04 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 58.5% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 188 through 202 removed outlier: 5.276A pdb=" N THR B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.864A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.224A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.501A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 340 through 353 removed outlier: 3.630A pdb=" N GLU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 393 through 412 Processing helix chain 'B' and resid 422 through 449 removed outlier: 4.032A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.756A pdb=" N PHE B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 496 Proline residue: B 485 - end of helix removed outlier: 5.063A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 528 removed outlier: 3.571A pdb=" N PHE B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 508 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 550 Processing helix chain 'B' and resid 553 through 556 No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 563 through 571 removed outlier: 4.186A pdb=" N TRP B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE B 571 " --> pdb=" O TRP B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 563 through 571' Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.640A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.465A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN B 629 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL B 631 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 649 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 188 through 202 removed outlier: 5.276A pdb=" N THR A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.863A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.225A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 4.501A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 340 through 353 removed outlier: 3.630A pdb=" N GLU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 393 through 412 Processing helix chain 'A' and resid 422 through 449 removed outlier: 4.033A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.756A pdb=" N PHE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 496 Proline residue: A 485 - end of helix removed outlier: 5.063A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 528 removed outlier: 3.571A pdb=" N PHE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 508 " --> pdb=" O ASP A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 Processing helix chain 'A' and resid 553 through 556 No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.186A pdb=" N TRP A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU A 568 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 571 " --> pdb=" O TRP A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 571' Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.639A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.466A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 629 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 649 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.319A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP B 210 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 124 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 256 through 260 removed outlier: 3.559A pdb=" N PHE B 266 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA B 260 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 69 through 71 Processing sheet with id= E, first strand: chain 'A' and resid 75 through 78 removed outlier: 6.320A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP A 210 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 124 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.558A pdb=" N PHE A 266 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 260 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2790 1.34 - 1.46: 2209 1.46 - 1.58: 4082 1.58 - 1.70: 22 1.70 - 1.82: 94 Bond restraints: 9197 Sorted by residual: bond pdb=" C5 ATP B 701 " pdb=" N7 ATP B 701 " ideal model delta sigma weight residual 1.387 1.525 -0.138 1.00e-02 1.00e+04 1.91e+02 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.525 -0.138 1.00e-02 1.00e+04 1.89e+02 bond pdb=" C6 ATP A 701 " pdb=" N6 ATP A 701 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.07e+02 bond pdb=" C6 ATP B 701 " pdb=" N6 ATP B 701 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.07e+02 bond pdb=" C4 ATP B 701 " pdb=" N9 ATP B 701 " ideal model delta sigma weight residual 1.374 1.273 0.101 1.00e-02 1.00e+04 1.01e+02 ... (remaining 9192 not shown) Histogram of bond angle deviations from ideal: 98.94 - 107.07: 266 107.07 - 115.19: 5631 115.19 - 123.32: 6332 123.32 - 131.44: 235 131.44 - 139.57: 15 Bond angle restraints: 12479 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 123.38 16.49 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.41 16.46 1.00e+00 1.00e+00 2.71e+02 angle pdb=" C4 ATP B 701 " pdb=" N9 ATP B 701 " pdb=" C8 ATP B 701 " ideal model delta sigma weight residual 105.72 121.17 -15.45 1.00e+00 1.00e+00 2.39e+02 angle pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " pdb=" C8 ATP A 701 " ideal model delta sigma weight residual 105.72 121.12 -15.40 1.00e+00 1.00e+00 2.37e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 122.59 14.24 1.00e+00 1.00e+00 2.03e+02 ... (remaining 12474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 4973 13.01 - 26.01: 396 26.01 - 39.02: 143 39.02 - 52.03: 43 52.03 - 65.03: 13 Dihedral angle restraints: 5568 sinusoidal: 2294 harmonic: 3274 Sorted by residual: dihedral pdb=" CA GLN A 181 " pdb=" C GLN A 181 " pdb=" N PHE A 182 " pdb=" CA PHE A 182 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLN B 181 " pdb=" C GLN B 181 " pdb=" N PHE B 182 " pdb=" CA PHE B 182 " ideal model delta harmonic sigma weight residual 180.00 160.18 19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY B 553 " pdb=" C GLY B 553 " pdb=" N LEU B 554 " pdb=" CA LEU B 554 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1387 0.095 - 0.189: 43 0.189 - 0.284: 9 0.284 - 0.378: 1 0.378 - 0.473: 1 Chirality restraints: 1441 Sorted by residual: chirality pdb=" C21 TTC A 702 " pdb=" C16 TTC A 702 " pdb=" C20 TTC A 702 " pdb=" O24 TTC A 702 " both_signs ideal model delta sigma weight residual False -2.50 -2.97 0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" C17 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C16 CLR B 702 " pdb=" C20 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C17 CLR A 703 " pdb=" C13 CLR A 703 " pdb=" C16 CLR A 703 " pdb=" C20 CLR A 703 " both_signs ideal model delta sigma weight residual False 2.55 2.84 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1438 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 TTC A 702 " 0.009 2.00e-02 2.50e+03 1.08e-02 6.44e+00 pdb=" C11 TTC A 702 " 0.001 2.00e-02 2.50e+03 pdb=" C13 TTC A 702 " 0.009 2.00e-02 2.50e+03 pdb=" C14 TTC A 702 " 0.008 2.00e-02 2.50e+03 pdb=" C15 TTC A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C16 TTC A 702 " 0.019 2.00e-02 2.50e+03 pdb=" C17 TTC A 702 " 0.007 2.00e-02 2.50e+03 pdb=" C19 TTC A 702 " -0.007 2.00e-02 2.50e+03 pdb=" C2 TTC A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C21 TTC A 702 " -0.033 2.00e-02 2.50e+03 pdb=" C27 TTC A 702 " -0.022 2.00e-02 2.50e+03 pdb=" C3 TTC A 702 " 0.010 2.00e-02 2.50e+03 pdb=" C4 TTC A 702 " 0.002 2.00e-02 2.50e+03 pdb=" C5 TTC A 702 " 0.001 2.00e-02 2.50e+03 pdb=" C6 TTC A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C7 TTC A 702 " -0.005 2.00e-02 2.50e+03 pdb=" C8 TTC A 702 " 0.001 2.00e-02 2.50e+03 pdb=" C9 TTC A 702 " -0.002 2.00e-02 2.50e+03 pdb=" N10 TTC A 702 " -0.007 2.00e-02 2.50e+03 pdb=" N12 TTC A 702 " 0.006 2.00e-02 2.50e+03 pdb=" O18 TTC A 702 " -0.001 2.00e-02 2.50e+03 pdb=" O26 TTC A 702 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO B 602 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 602 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.018 5.00e-02 4.00e+02 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1868 2.77 - 3.30: 8854 3.30 - 3.84: 14158 3.84 - 4.37: 17223 4.37 - 4.90: 29756 Nonbonded interactions: 71859 Sorted by model distance: nonbonded pdb=" OG SER B 384 " pdb=" OD1 ASP B 477 " model vdw 2.240 2.440 nonbonded pdb=" OG SER A 384 " pdb=" OD1 ASP A 477 " model vdw 2.240 2.440 nonbonded pdb=" CE MET A 549 " pdb=" O24 TTC A 702 " model vdw 2.252 3.460 nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASP B 98 " model vdw 2.309 2.440 nonbonded pdb=" OH TYR A 44 " pdb=" OD1 ASP A 98 " model vdw 2.310 2.440 ... (remaining 71854 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 34 through 654 or resid 701)) selection = (chain 'B' and (resid 34 through 654 or resid 701)) } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.200 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.480 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.011 0.195 9197 Z= 0.695 Angle : 0.898 16.490 12479 Z= 0.597 Chirality : 0.047 0.473 1441 Planarity : 0.003 0.033 1530 Dihedral : 11.822 65.035 3459 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.52 % Allowed : 3.00 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1122 helix: 1.41 (0.20), residues: 668 sheet: -0.59 (0.73), residues: 48 loop : -1.66 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 564 HIS 0.004 0.001 HIS A 267 PHE 0.012 0.001 PHE B 39 TYR 0.008 0.001 TYR B 469 ARG 0.003 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 207 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: B 296 ASP cc_start: 0.7260 (t70) cc_final: 0.6748 (t0) outliers start: 5 outliers final: 2 residues processed: 212 average time/residue: 0.2415 time to fit residues: 68.0547 Evaluate side-chains 104 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN A 126 GLN A 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9197 Z= 0.261 Angle : 0.578 8.118 12479 Z= 0.309 Chirality : 0.042 0.179 1441 Planarity : 0.005 0.031 1530 Dihedral : 8.632 60.201 1435 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.38 % Allowed : 7.33 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1122 helix: 1.47 (0.21), residues: 668 sheet: 0.09 (0.77), residues: 48 loop : -1.69 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 379 HIS 0.005 0.001 HIS A 267 PHE 0.017 0.002 PHE A 506 TYR 0.011 0.001 TYR A 44 ARG 0.004 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 126 average time/residue: 0.1975 time to fit residues: 35.4656 Evaluate side-chains 106 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.0670 chunk 100 optimal weight: 2.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9197 Z= 0.384 Angle : 0.606 6.020 12479 Z= 0.322 Chirality : 0.044 0.209 1441 Planarity : 0.005 0.034 1530 Dihedral : 8.619 63.891 1435 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.89 % Allowed : 9.19 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1122 helix: 1.24 (0.20), residues: 666 sheet: 0.21 (0.72), residues: 50 loop : -1.85 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 379 HIS 0.004 0.001 HIS A 267 PHE 0.018 0.002 PHE A 293 TYR 0.015 0.002 TYR A 287 ARG 0.006 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8364 (tp) REVERT: B 341 PHE cc_start: 0.8036 (m-10) cc_final: 0.7764 (m-80) outliers start: 28 outliers final: 20 residues processed: 119 average time/residue: 0.1911 time to fit residues: 33.5963 Evaluate side-chains 107 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9197 Z= 0.152 Angle : 0.479 6.576 12479 Z= 0.258 Chirality : 0.038 0.178 1441 Planarity : 0.004 0.032 1530 Dihedral : 7.889 66.555 1435 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.69 % Allowed : 11.16 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1122 helix: 1.52 (0.21), residues: 674 sheet: 0.85 (0.76), residues: 48 loop : -1.84 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.002 0.001 HIS A 267 PHE 0.014 0.001 PHE A 293 TYR 0.009 0.001 TYR B 336 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: B 107 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7750 (mt) REVERT: A 71 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.6821 (mtt) REVERT: A 172 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7566 (mtmm) outliers start: 26 outliers final: 16 residues processed: 115 average time/residue: 0.1846 time to fit residues: 31.0744 Evaluate side-chains 100 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 504 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 0.0050 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9197 Z= 0.153 Angle : 0.463 6.080 12479 Z= 0.247 Chirality : 0.037 0.132 1441 Planarity : 0.004 0.033 1530 Dihedral : 7.333 70.384 1434 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.58 % Allowed : 11.26 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1122 helix: 1.67 (0.21), residues: 674 sheet: 1.09 (0.75), residues: 48 loop : -1.83 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.002 0.001 HIS A 267 PHE 0.016 0.001 PHE B 293 TYR 0.009 0.001 TYR B 336 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.022 Fit side-chains REVERT: B 592 CYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6571 (m) REVERT: A 172 LYS cc_start: 0.7965 (mmmm) cc_final: 0.7579 (mtmm) outliers start: 25 outliers final: 15 residues processed: 110 average time/residue: 0.1783 time to fit residues: 29.3127 Evaluate side-chains 96 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0060 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9197 Z= 0.197 Angle : 0.477 6.888 12479 Z= 0.253 Chirality : 0.038 0.139 1441 Planarity : 0.004 0.033 1530 Dihedral : 7.356 70.741 1433 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.58 % Allowed : 11.36 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1122 helix: 1.67 (0.21), residues: 674 sheet: 1.06 (0.74), residues: 50 loop : -1.89 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS A 267 PHE 0.014 0.001 PHE B 293 TYR 0.008 0.001 TYR B 336 ARG 0.002 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (tt) REVERT: A 71 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.6876 (mtt) REVERT: A 172 LYS cc_start: 0.8042 (mmmm) cc_final: 0.7589 (mtmm) outliers start: 25 outliers final: 19 residues processed: 102 average time/residue: 0.1850 time to fit residues: 28.0873 Evaluate side-chains 99 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9197 Z= 0.130 Angle : 0.449 8.089 12479 Z= 0.237 Chirality : 0.036 0.135 1441 Planarity : 0.003 0.033 1530 Dihedral : 7.420 72.938 1433 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 12.50 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1122 helix: 1.84 (0.21), residues: 674 sheet: 1.30 (0.76), residues: 50 loop : -1.71 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.002 0.000 HIS A 267 PHE 0.013 0.001 PHE A 506 TYR 0.008 0.001 TYR B 336 ARG 0.002 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.173 Fit side-chains REVERT: B 207 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8305 (tt) REVERT: B 592 CYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6574 (m) REVERT: A 71 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6726 (mtt) REVERT: A 172 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7607 (mtmm) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.1857 time to fit residues: 26.3042 Evaluate side-chains 91 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.0218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9197 Z= 0.184 Angle : 0.470 8.900 12479 Z= 0.247 Chirality : 0.038 0.137 1441 Planarity : 0.004 0.033 1530 Dihedral : 7.736 72.755 1433 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.96 % Allowed : 13.22 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1122 helix: 1.99 (0.21), residues: 656 sheet: 1.41 (0.75), residues: 50 loop : -1.72 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS A 267 PHE 0.013 0.001 PHE A 506 TYR 0.009 0.001 TYR B 336 ARG 0.002 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 71 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.6852 (mtt) outliers start: 19 outliers final: 17 residues processed: 95 average time/residue: 0.1967 time to fit residues: 27.2605 Evaluate side-chains 96 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN A 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9197 Z= 0.312 Angle : 0.554 10.594 12479 Z= 0.288 Chirality : 0.040 0.140 1441 Planarity : 0.004 0.032 1530 Dihedral : 7.965 71.634 1433 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1122 helix: 1.71 (0.21), residues: 660 sheet: 1.22 (0.74), residues: 50 loop : -1.85 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 624 HIS 0.004 0.001 HIS A 243 PHE 0.014 0.002 PHE A 506 TYR 0.011 0.002 TYR A 494 ARG 0.003 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: B 207 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 71 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7097 (mtt) outliers start: 22 outliers final: 18 residues processed: 93 average time/residue: 0.1910 time to fit residues: 25.7469 Evaluate side-chains 95 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 654 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.0270 chunk 73 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9197 Z= 0.143 Angle : 0.472 11.416 12479 Z= 0.247 Chirality : 0.037 0.134 1441 Planarity : 0.004 0.034 1530 Dihedral : 7.764 74.686 1433 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.76 % Allowed : 14.26 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1122 helix: 1.97 (0.21), residues: 656 sheet: 1.53 (0.77), residues: 50 loop : -1.65 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.003 0.001 HIS A 267 PHE 0.013 0.001 PHE A 506 TYR 0.008 0.001 TYR B 336 ARG 0.002 0.000 ARG A 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.083 Fit side-chains REVERT: B 207 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8302 (tt) REVERT: B 592 CYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6492 (m) REVERT: A 71 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.6784 (mtt) REVERT: A 172 LYS cc_start: 0.8113 (mmmm) cc_final: 0.7560 (mtmm) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 0.1937 time to fit residues: 26.9198 Evaluate side-chains 97 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.0010 chunk 13 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 78 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 overall best weight: 0.0538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113667 restraints weight = 11714.235| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.82 r_work: 0.3267 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9197 Z= 0.117 Angle : 0.455 10.696 12479 Z= 0.238 Chirality : 0.036 0.133 1441 Planarity : 0.004 0.034 1530 Dihedral : 7.399 77.333 1433 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.55 % Allowed : 14.46 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1122 helix: 2.02 (0.21), residues: 670 sheet: 1.70 (0.78), residues: 50 loop : -1.60 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.002 0.000 HIS B 375 PHE 0.022 0.001 PHE B 293 TYR 0.007 0.001 TYR B 336 ARG 0.002 0.000 ARG A 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2150.51 seconds wall clock time: 39 minutes 31.35 seconds (2371.35 seconds total)