Starting phenix.real_space_refine on Thu Mar 14 15:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/03_2024/6hbu_0190_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/03_2024/6hbu_0190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/03_2024/6hbu_0190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/03_2024/6hbu_0190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/03_2024/6hbu_0190_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/03_2024/6hbu_0190_updated.pdb" } resolution = 3.09 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= 0.001 sd= 0.011 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 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5910 2.51 5 N 1512 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9146 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4541 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 20, 'TRANS': 563} Chain breaks: 3 Chain: "B" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4541 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 20, 'TRANS': 563} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.37, per 1000 atoms: 0.59 Number of scatterers: 9146 At special positions: 0 Unit cell: (81.81, 89.91, 132.84, 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 58 16.00 P 6 15.00 Mg 2 11.99 O 1658 8.00 N 1512 7.00 C 5910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.01 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 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: 3.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 4 sheets defined 50.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.542A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 218 through 234 removed outlier: 3.694A pdb=" N ASN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.150A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.718A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 340 through 352 removed outlier: 3.555A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.506A pdb=" N ARG A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 Processing helix chain 'A' and resid 423 through 447 removed outlier: 4.106A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 466 through 478 removed outlier: 3.651A pdb=" N LEU A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.767A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 528 Processing helix chain 'A' and resid 535 through 550 removed outlier: 3.690A pdb=" N LEU A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.508A pdb=" N LEU A 626 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS A 628 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A 630 " --> pdb=" O TRP A 627 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 631 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 632 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 633 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 634 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A 635 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 638 " --> pdb=" O CYS A 635 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 639 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 641 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 643 " --> pdb=" O PHE A 640 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 644 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 647 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.542A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.695A pdb=" N ASN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.149A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 277 No H-bonds generated for 'chain 'B' and resid 274 through 277' Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.717A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 328 through 337 Processing helix chain 'B' and resid 340 through 352 removed outlier: 3.555A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 removed outlier: 3.506A pdb=" N ARG B 378 " --> pdb=" O CYS B 374 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 412 Processing helix chain 'B' and resid 423 through 447 removed outlier: 4.105A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 466 through 478 removed outlier: 3.652A pdb=" N LEU B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 477 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.768A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 528 Processing helix chain 'B' and resid 535 through 550 removed outlier: 3.690A pdb=" N LEU B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.508A pdb=" N LEU B 626 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS B 628 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 630 " --> pdb=" O TRP B 627 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 631 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 632 " --> pdb=" O ASN B 629 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 633 " --> pdb=" O HIS B 630 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 634 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 638 " --> pdb=" O CYS B 635 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE B 639 " --> pdb=" O MET B 636 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 641 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 643 " --> pdb=" O PHE B 640 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 644 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS B 647 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.446A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY A 80 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= D, first strand: chain 'B' and resid 263 through 268 removed outlier: 6.446A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1032 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: 2.44 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2434 1.33 - 1.45: 1814 1.45 - 1.57: 4984 1.57 - 1.70: 10 1.70 - 1.82: 94 Bond restraints: 9336 Sorted by residual: bond pdb=" C4 ATP B1501 " pdb=" C5 ATP B1501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C4 ATP A1501 " pdb=" C5 ATP A1501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C5 ATP B1501 " pdb=" C6 ATP B1501 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.06e+01 bond pdb=" C5 ATP A1501 " pdb=" C6 ATP A1501 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.05e+01 bond pdb=" C4 ATP B1501 " pdb=" N9 ATP B1501 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.50e+01 ... (remaining 9331 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.88: 212 105.88 - 113.37: 5127 113.37 - 120.86: 4534 120.86 - 128.35: 2704 128.35 - 135.84: 71 Bond angle restraints: 12648 Sorted by residual: angle pdb=" PB ATP B1501 " pdb=" O3B ATP B1501 " pdb=" PG ATP B1501 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 121.74 18.13 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PA ATP B1501 " pdb=" O3A ATP B1501 " pdb=" PB ATP B1501 " ideal model delta sigma weight residual 136.83 123.39 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 123.43 13.40 1.00e+00 1.00e+00 1.80e+02 angle pdb=" C5 ATP B1501 " pdb=" C4 ATP B1501 " pdb=" N3 ATP B1501 " ideal model delta sigma weight residual 126.80 119.17 7.63 1.00e+00 1.00e+00 5.82e+01 ... (remaining 12643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 5200 15.33 - 30.67: 270 30.67 - 46.00: 78 46.00 - 61.33: 21 61.33 - 76.67: 10 Dihedral angle restraints: 5579 sinusoidal: 2211 harmonic: 3368 Sorted by residual: dihedral pdb=" CA ASN B 604 " pdb=" C ASN B 604 " pdb=" N TYR B 605 " pdb=" CA TYR B 605 " ideal model delta harmonic sigma weight residual 180.00 108.75 71.25 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ASN A 604 " pdb=" C ASN A 604 " pdb=" N TYR A 605 " pdb=" CA TYR A 605 " ideal model delta harmonic sigma weight residual 180.00 108.79 71.21 0 5.00e+00 4.00e-02 2.03e+02 dihedral pdb=" CA ALA B 115 " pdb=" C ALA B 115 " pdb=" N ASN B 116 " pdb=" CA ASN B 116 " ideal model delta harmonic sigma weight residual 180.00 123.00 57.00 0 5.00e+00 4.00e-02 1.30e+02 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1213 0.075 - 0.150: 230 0.150 - 0.226: 14 0.226 - 0.301: 7 0.301 - 0.376: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA GLN B 589 " pdb=" N GLN B 589 " pdb=" C GLN B 589 " pdb=" CB GLN B 589 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA GLN A 589 " pdb=" N GLN A 589 " pdb=" C GLN A 589 " pdb=" CB GLN A 589 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU A 225 " pdb=" CB LEU A 225 " pdb=" CD1 LEU A 225 " pdb=" CD2 LEU A 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1463 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 602 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 602 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 588 " -0.013 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C GLY A 588 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY A 588 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN A 589 " -0.016 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 50 2.55 - 3.14: 6642 3.14 - 3.73: 13986 3.73 - 4.31: 21403 4.31 - 4.90: 34809 Nonbonded interactions: 76890 Sorted by model distance: nonbonded pdb=" CE LYS B 500 " pdb=" OE1 GLN B 589 " model vdw 1.965 3.440 nonbonded pdb=" CE LYS A 500 " pdb=" OE1 GLN A 589 " model vdw 1.977 3.440 nonbonded pdb=" NH2 ARG B 184 " pdb=" O1A ATP A1501 " model vdw 2.315 2.520 nonbonded pdb=" OG1 THR A 133 " pdb=" ND2 ASN A 387 " model vdw 2.373 2.520 nonbonded pdb=" OG1 THR B 133 " pdb=" ND2 ASN B 387 " model vdw 2.374 2.520 ... (remaining 76885 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' selection = chain 'B' } 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: 0.690 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: 3.920 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.750 Find NCS groups from input model: 0.480 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: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 0.074 9336 Z= 0.574 Angle : 1.177 18.132 12648 Z= 0.683 Chirality : 0.060 0.376 1466 Planarity : 0.008 0.102 1566 Dihedral : 11.560 76.667 3406 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.86 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.71 % 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: -5.40 (0.17), residues: 1152 helix: -4.20 (0.10), residues: 648 sheet: -1.86 (0.42), residues: 76 loop : -2.49 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 624 HIS 0.013 0.003 HIS A 583 PHE 0.032 0.003 PHE A 578 TYR 0.039 0.003 TYR A 463 ARG 0.010 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.024 Fit side-chains REVERT: A 251 LYS cc_start: 0.8156 (ttpm) cc_final: 0.7946 (mtpt) REVERT: A 451 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7597 (tt0) REVERT: B 451 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7475 (tt0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2431 time to fit residues: 60.7249 Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 166 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 437 GLN A 557 ASN A 583 HIS B 154 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN B 437 GLN B 531 GLN B 557 ASN B 583 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9336 Z= 0.198 Angle : 0.661 7.964 12648 Z= 0.342 Chirality : 0.043 0.154 1466 Planarity : 0.006 0.087 1566 Dihedral : 9.522 77.279 1314 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % Rotamer: Outliers : 1.61 % Allowed : 7.43 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1152 helix: -1.76 (0.17), residues: 630 sheet: -1.29 (0.48), residues: 86 loop : -2.05 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.005 0.001 HIS B 243 PHE 0.013 0.001 PHE A 578 TYR 0.015 0.001 TYR B 605 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.987 Fit side-chains REVERT: A 71 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.6905 (mtt) REVERT: A 105 ASP cc_start: 0.7921 (p0) cc_final: 0.7588 (p0) REVERT: A 206 ILE cc_start: 0.8870 (mt) cc_final: 0.8634 (mt) REVERT: A 251 LYS cc_start: 0.8102 (ttpm) cc_final: 0.7871 (mtpt) REVERT: A 451 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7542 (tt0) REVERT: B 105 ASP cc_start: 0.7726 (p0) cc_final: 0.7409 (p0) REVERT: B 451 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7482 (tt0) outliers start: 16 outliers final: 11 residues processed: 135 average time/residue: 0.1895 time to fit residues: 37.4425 Evaluate side-chains 110 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 299 ASN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 9336 Z= 0.590 Angle : 0.845 10.099 12648 Z= 0.420 Chirality : 0.053 0.208 1466 Planarity : 0.006 0.090 1566 Dihedral : 9.651 78.084 1314 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.91 % Allowed : 8.33 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -1.77 (0.24), residues: 1152 helix: -0.77 (0.19), residues: 654 sheet: -0.43 (0.54), residues: 68 loop : -1.79 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 627 HIS 0.008 0.002 HIS A 375 PHE 0.022 0.003 PHE B 489 TYR 0.021 0.003 TYR B 123 ARG 0.005 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 1.212 Fit side-chains REVERT: A 105 ASP cc_start: 0.8052 (p0) cc_final: 0.7709 (p0) REVERT: A 251 LYS cc_start: 0.8207 (ttpm) cc_final: 0.7946 (mtpt) REVERT: A 378 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7349 (mtm-85) REVERT: A 451 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7536 (tt0) REVERT: B 105 ASP cc_start: 0.7822 (p0) cc_final: 0.7476 (p0) REVERT: B 172 LYS cc_start: 0.8312 (ptmt) cc_final: 0.8058 (pttt) REVERT: B 378 ARG cc_start: 0.7486 (mtm180) cc_final: 0.7273 (mtm-85) REVERT: B 451 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7463 (tt0) outliers start: 29 outliers final: 19 residues processed: 122 average time/residue: 0.2002 time to fit residues: 34.7693 Evaluate side-chains 120 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN B 436 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9336 Z= 0.194 Angle : 0.617 8.193 12648 Z= 0.315 Chirality : 0.042 0.148 1466 Planarity : 0.005 0.080 1566 Dihedral : 9.173 74.088 1314 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % Rotamer: Outliers : 1.91 % Allowed : 10.54 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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 (0.25), residues: 1152 helix: 0.06 (0.21), residues: 652 sheet: -0.17 (0.56), residues: 68 loop : -1.57 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS B 243 PHE 0.013 0.001 PHE B 489 TYR 0.012 0.001 TYR B 605 ARG 0.002 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.993 Fit side-chains REVERT: A 105 ASP cc_start: 0.7874 (p0) cc_final: 0.7448 (p0) REVERT: A 251 LYS cc_start: 0.8148 (ttpm) cc_final: 0.7910 (mtpt) REVERT: A 451 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7536 (tt0) REVERT: B 105 ASP cc_start: 0.7648 (p0) cc_final: 0.7352 (p0) REVERT: B 172 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7993 (pttt) REVERT: B 451 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7459 (tt0) outliers start: 19 outliers final: 15 residues processed: 113 average time/residue: 0.2008 time to fit residues: 32.4714 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9336 Z= 0.382 Angle : 0.693 8.740 12648 Z= 0.349 Chirality : 0.046 0.158 1466 Planarity : 0.005 0.082 1566 Dihedral : 9.095 72.811 1314 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.47 % Favored : 94.36 % Rotamer: Outliers : 2.91 % Allowed : 10.54 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -0.77 (0.25), residues: 1152 helix: 0.14 (0.21), residues: 654 sheet: -0.04 (0.56), residues: 68 loop : -1.51 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS A 375 PHE 0.014 0.002 PHE A 489 TYR 0.017 0.002 TYR B 123 ARG 0.003 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.967 Fit side-chains REVERT: A 64 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 105 ASP cc_start: 0.7942 (p0) cc_final: 0.7447 (p0) REVERT: A 251 LYS cc_start: 0.8177 (ttpm) cc_final: 0.7931 (mtpt) REVERT: A 451 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7513 (tt0) REVERT: B 64 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 105 ASP cc_start: 0.7706 (p0) cc_final: 0.7236 (p0) REVERT: B 172 LYS cc_start: 0.8330 (ptmt) cc_final: 0.8050 (pttt) REVERT: B 451 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7469 (tt0) outliers start: 29 outliers final: 20 residues processed: 124 average time/residue: 0.2051 time to fit residues: 36.6577 Evaluate side-chains 116 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9336 Z= 0.197 Angle : 0.594 8.077 12648 Z= 0.303 Chirality : 0.042 0.143 1466 Planarity : 0.004 0.077 1566 Dihedral : 8.772 68.076 1314 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % Rotamer: Outliers : 2.01 % Allowed : 12.15 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -0.40 (0.26), residues: 1152 helix: 0.50 (0.21), residues: 654 sheet: -0.14 (0.55), residues: 68 loop : -1.41 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.003 0.001 HIS B 375 PHE 0.010 0.001 PHE A 489 TYR 0.012 0.001 TYR B 605 ARG 0.003 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.130 Fit side-chains REVERT: A 64 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 105 ASP cc_start: 0.7800 (p0) cc_final: 0.7326 (p0) REVERT: A 251 LYS cc_start: 0.8154 (ttpm) cc_final: 0.7937 (mtpt) REVERT: A 451 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7517 (tt0) REVERT: B 64 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 105 ASP cc_start: 0.7572 (p0) cc_final: 0.7163 (p0) REVERT: B 451 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7443 (tt0) outliers start: 20 outliers final: 18 residues processed: 111 average time/residue: 0.1976 time to fit residues: 32.2770 Evaluate side-chains 111 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9336 Z= 0.231 Angle : 0.601 7.990 12648 Z= 0.306 Chirality : 0.042 0.147 1466 Planarity : 0.004 0.077 1566 Dihedral : 8.615 65.922 1314 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % Rotamer: Outliers : 2.41 % Allowed : 12.35 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -0.25 (0.26), residues: 1152 helix: 0.57 (0.21), residues: 660 sheet: -0.07 (0.55), residues: 68 loop : -1.29 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS B 375 PHE 0.011 0.001 PHE A 489 TYR 0.010 0.001 TYR B 605 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.089 Fit side-chains REVERT: A 64 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8206 (mp) REVERT: A 105 ASP cc_start: 0.7811 (p0) cc_final: 0.7338 (p0) REVERT: A 251 LYS cc_start: 0.8154 (ttpm) cc_final: 0.7935 (mtpt) REVERT: A 451 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7504 (tt0) REVERT: B 64 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 105 ASP cc_start: 0.7597 (p0) cc_final: 0.7180 (p0) REVERT: B 451 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7415 (tt0) outliers start: 24 outliers final: 18 residues processed: 113 average time/residue: 0.1891 time to fit residues: 31.0872 Evaluate side-chains 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 126 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9336 Z= 0.463 Angle : 0.724 9.637 12648 Z= 0.361 Chirality : 0.048 0.168 1466 Planarity : 0.005 0.076 1566 Dihedral : 8.862 67.992 1314 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % Rotamer: Outliers : 2.71 % Allowed : 12.15 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -0.56 (0.25), residues: 1152 helix: 0.29 (0.21), residues: 662 sheet: 0.04 (0.53), residues: 72 loop : -1.43 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.004 0.001 HIS B 375 PHE 0.014 0.002 PHE A 39 TYR 0.013 0.002 TYR B 459 ARG 0.006 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.043 Fit side-chains REVERT: A 64 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 105 ASP cc_start: 0.7916 (p0) cc_final: 0.7421 (p0) REVERT: A 251 LYS cc_start: 0.8124 (ttpm) cc_final: 0.7912 (mtpt) REVERT: A 451 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7519 (tt0) REVERT: B 64 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8181 (mp) REVERT: B 105 ASP cc_start: 0.7730 (p0) cc_final: 0.7255 (p0) REVERT: B 451 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7461 (tt0) outliers start: 27 outliers final: 19 residues processed: 120 average time/residue: 0.1998 time to fit residues: 34.5133 Evaluate side-chains 116 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 609 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9336 Z= 0.183 Angle : 0.586 7.985 12648 Z= 0.298 Chirality : 0.041 0.147 1466 Planarity : 0.004 0.075 1566 Dihedral : 8.569 64.681 1314 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 1.71 % Allowed : 14.06 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -0.15 (0.26), residues: 1152 helix: 0.74 (0.21), residues: 654 sheet: -0.06 (0.54), residues: 72 loop : -1.38 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.004 0.001 HIS B 375 PHE 0.009 0.001 PHE A 489 TYR 0.011 0.001 TYR B 605 ARG 0.001 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.096 Fit side-chains REVERT: A 64 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 105 ASP cc_start: 0.7754 (p0) cc_final: 0.7289 (p0) REVERT: A 251 LYS cc_start: 0.8160 (ttpm) cc_final: 0.7936 (mtpt) REVERT: A 451 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7522 (tt0) REVERT: B 105 ASP cc_start: 0.7534 (p0) cc_final: 0.7165 (p0) REVERT: B 451 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7446 (tt0) outliers start: 17 outliers final: 15 residues processed: 109 average time/residue: 0.2064 time to fit residues: 32.0806 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 299 ASN A 590 ASN B 126 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9336 Z= 0.345 Angle : 0.652 8.878 12648 Z= 0.328 Chirality : 0.045 0.158 1466 Planarity : 0.005 0.075 1566 Dihedral : 8.687 66.730 1314 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 1.91 % Allowed : 13.76 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -0.26 (0.26), residues: 1152 helix: 0.56 (0.21), residues: 660 sheet: 0.03 (0.54), residues: 72 loop : -1.33 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.004 0.001 HIS B 375 PHE 0.012 0.001 PHE A 489 TYR 0.011 0.002 TYR B 459 ARG 0.004 0.000 ARG A 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.030 Fit side-chains REVERT: A 64 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 105 ASP cc_start: 0.7836 (p0) cc_final: 0.7356 (p0) REVERT: A 251 LYS cc_start: 0.8122 (ttpm) cc_final: 0.7919 (mtpt) REVERT: A 299 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8780 (t0) REVERT: A 451 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7511 (tt0) REVERT: B 64 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 105 ASP cc_start: 0.7635 (p0) cc_final: 0.7205 (p0) REVERT: B 451 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7453 (tt0) outliers start: 19 outliers final: 15 residues processed: 112 average time/residue: 0.2117 time to fit residues: 34.0785 Evaluate side-chains 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 589 GLN A 590 ASN B 126 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.136121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119796 restraints weight = 9627.787| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.78 r_work: 0.3025 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9336 Z= 0.202 Angle : 0.601 8.087 12648 Z= 0.305 Chirality : 0.042 0.172 1466 Planarity : 0.004 0.075 1566 Dihedral : 8.594 65.430 1314 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 1.91 % Allowed : 13.86 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.53 % 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: -0.08 (0.26), residues: 1152 helix: 0.78 (0.21), residues: 654 sheet: -0.07 (0.54), residues: 72 loop : -1.31 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS B 375 PHE 0.010 0.001 PHE A 489 TYR 0.010 0.001 TYR B 605 ARG 0.002 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.35 seconds wall clock time: 35 minutes 0.20 seconds (2100.20 seconds total)