Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 06:18:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/04_2023/6hbu_0190_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/04_2023/6hbu_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_0190/04_2023/6hbu_0190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/04_2023/6hbu_0190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/04_2023/6hbu_0190_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hbu_0190/04_2023/6hbu_0190_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.93, per 1000 atoms: 0.54 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: 3.66 Conformation dependent library (CDL) restraints added in 1.6 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: 1.05 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: 2.55 Time building geometry restraints manager: 3.92 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: 5168 15.33 - 30.67: 252 30.67 - 46.00: 74 46.00 - 61.33: 15 61.33 - 76.67: 8 Dihedral angle restraints: 5517 sinusoidal: 2149 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 5514 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: 1.570 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: 4.320 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.920 Find NCS groups from input model: 0.450 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- 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 : 11.063 76.667 3344 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 % 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 *********************** 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 : 1.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2513 time to fit residues: 62.3433 Evaluate side-chains 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5959 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8308 moved from start: 0.1790 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= 0.203 Angle : 0.677 8.130 12648 Z= 0.350 Chirality : 0.043 0.149 1466 Planarity : 0.006 0.088 1566 Dihedral : 7.657 85.816 1252 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % Rotamer Outliers : 1.61 % 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: -2.95 (0.21), residues: 1152 helix: -1.82 (0.17), residues: 630 sheet: -1.29 (0.48), residues: 86 loop : -2.05 (0.28), residues: 436 *********************** 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 141 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.138 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 136 average time/residue: 0.1866 time to fit residues: 37.0220 Evaluate side-chains 105 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0856 time to fit residues: 3.2562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 0.0570 overall best weight: 0.9504 ------------------------------------------------------------------------------- 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 211 GLN A 299 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN B 436 ASN B 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9336 Z= 0.205 Angle : 0.632 8.000 12648 Z= 0.322 Chirality : 0.043 0.146 1466 Planarity : 0.005 0.087 1566 Dihedral : 7.235 82.124 1252 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer Outliers : 1.31 % 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: -1.28 (0.24), residues: 1152 helix: -0.25 (0.20), residues: 642 sheet: -1.20 (0.50), residues: 88 loop : -1.57 (0.30), residues: 422 *********************** 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 113 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.110 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 111 average time/residue: 0.1982 time to fit residues: 32.4338 Evaluate side-chains 100 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0910 time to fit residues: 2.7731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.8413 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 9336 Z= 0.414 Angle : 0.724 8.710 12648 Z= 0.364 Chirality : 0.047 0.162 1466 Planarity : 0.005 0.078 1566 Dihedral : 7.240 80.117 1252 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.12 % Favored : 94.53 % Rotamer Outliers : 1.10 % 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: -0.90 (0.25), residues: 1152 helix: 0.03 (0.21), residues: 640 sheet: -0.49 (0.52), residues: 68 loop : -1.45 (0.30), residues: 444 *********************** 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 115 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.062 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.2136 time to fit residues: 33.2256 Evaluate side-chains 101 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0942 time to fit residues: 2.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8355 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9336 Z= 0.181 Angle : 0.594 7.937 12648 Z= 0.304 Chirality : 0.042 0.145 1466 Planarity : 0.004 0.080 1566 Dihedral : 6.908 79.599 1252 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer Outliers : 1.00 % 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: -0.41 (0.25), residues: 1152 helix: 0.49 (0.21), residues: 648 sheet: -0.42 (0.54), residues: 68 loop : -1.33 (0.31), residues: 436 *********************** 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 105 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.159 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.1956 time to fit residues: 30.7014 Evaluate side-chains 92 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0824 time to fit residues: 2.4629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 65 optimal weight: 0.0270 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 0.0770 overall best weight: 1.6202 ------------------------------------------------------------------------------- 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: 0.8390 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9336 Z= 0.285 Angle : 0.638 8.230 12648 Z= 0.323 Chirality : 0.044 0.149 1466 Planarity : 0.005 0.075 1566 Dihedral : 6.872 77.978 1252 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.30 % Favored : 94.53 % Rotamer Outliers : 0.70 % 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: -0.38 (0.25), residues: 1152 helix: 0.50 (0.21), residues: 654 sheet: -0.25 (0.54), residues: 68 loop : -1.35 (0.31), residues: 430 *********************** 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 100 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.025 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 97 average time/residue: 0.2039 time to fit residues: 29.2696 Evaluate side-chains 92 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1166 time to fit residues: 2.1127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8438 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 9336 Z= 0.437 Angle : 0.725 8.819 12648 Z= 0.362 Chirality : 0.047 0.168 1466 Planarity : 0.005 0.077 1566 Dihedral : 7.026 72.821 1252 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.44 % Rotamer Outliers : 0.60 % 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: -0.58 (0.25), residues: 1152 helix: 0.30 (0.21), residues: 654 sheet: -0.13 (0.55), residues: 68 loop : -1.43 (0.31), residues: 430 *********************** 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 104 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.134 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 102 average time/residue: 0.2183 time to fit residues: 32.0828 Evaluate side-chains 95 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0875 time to fit residues: 2.0101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9336 Z= 0.188 Angle : 0.593 7.977 12648 Z= 0.303 Chirality : 0.041 0.185 1466 Planarity : 0.004 0.073 1566 Dihedral : 6.697 74.512 1252 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer Outliers : 0.20 % 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: -0.19 (0.26), residues: 1152 helix: 0.63 (0.21), residues: 660 sheet: -0.16 (0.56), residues: 68 loop : -1.27 (0.32), residues: 424 *********************** 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 95 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 1.154 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.2170 time to fit residues: 30.3001 Evaluate side-chains 90 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0913 time to fit residues: 1.7028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** A 299 ASN B 126 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 9336 Z= 0.296 Angle : 0.638 8.243 12648 Z= 0.323 Chirality : 0.044 0.235 1466 Planarity : 0.004 0.075 1566 Dihedral : 6.736 73.744 1252 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.86 % Favored : 94.97 % Rotamer Outliers : 0.70 % 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: -0.18 (0.26), residues: 1152 helix: 0.60 (0.21), residues: 660 sheet: -0.01 (0.57), residues: 68 loop : -1.21 (0.32), residues: 424 *********************** 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 98 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.048 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 94 average time/residue: 0.2230 time to fit residues: 30.1165 Evaluate side-chains 94 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0881 time to fit residues: 2.3418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 106 optimal weight: 0.0470 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- 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** A 299 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9336 Z= 0.177 Angle : 0.584 7.888 12648 Z= 0.299 Chirality : 0.041 0.188 1466 Planarity : 0.004 0.072 1566 Dihedral : 6.514 73.927 1252 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer Outliers : 0.00 % 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: 0.09 (0.26), residues: 1152 helix: 0.92 (0.21), residues: 654 sheet: -0.06 (0.57), residues: 68 loop : -1.22 (0.32), residues: 430 ********************** 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 94 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2164 time to fit residues: 29.5405 Evaluate side-chains 88 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 0.0570 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.134994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.118856 restraints weight = 9656.897| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 0.76 r_work: 0.3014 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 9336 Z= 0.356 Angle : 0.667 8.380 12648 Z= 0.336 Chirality : 0.045 0.234 1466 Planarity : 0.005 0.074 1566 Dihedral : 6.697 73.055 1252 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer Outliers : 0.30 % 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 (0.25), residues: 1152 helix: 0.71 (0.21), residues: 654 sheet: 0.08 (0.57), residues: 68 loop : -1.19 (0.32), residues: 430 =============================================================================== Job complete usr+sys time: 1822.49 seconds wall clock time: 34 minutes 9.67 seconds (2049.67 seconds total)