Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 23:03:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/07_2023/7xer_33158_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/07_2023/7xer_33158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/07_2023/7xer_33158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/07_2023/7xer_33158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/07_2023/7xer_33158_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/07_2023/7xer_33158_updated.pdb" } resolution = 2.47 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13168 2.51 5 N 3368 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B ASP 590": "OD1" <-> "OD2" Residue "B ASP 695": "OD1" <-> "OD2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C ASP 590": "OD1" <-> "OD2" Residue "C ASP 695": "OD1" <-> "OD2" Residue "C GLU 703": "OE1" <-> "OE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D ASP 590": "OD1" <-> "OD2" Residue "D ASP 695": "OD1" <-> "OD2" Residue "D GLU 703": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 20084 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 4993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4993 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.72, per 1000 atoms: 0.48 Number of scatterers: 20084 At special positions: 0 Unit cell: (156.156, 155.142, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3440 8.00 N 3368 7.00 C 13168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.97 Conformation dependent library (CDL) restraints added in 2.8 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 55.0% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 90 through 96 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 129 through 140 Proline residue: A 133 - end of helix removed outlier: 4.811A pdb=" N GLN A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 172 through 180 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.733A pdb=" N LEU A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 256 through 276 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.590A pdb=" N MET A 367 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 407 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 424 through 453 Processing helix chain 'A' and resid 468 through 487 removed outlier: 3.807A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 511 removed outlier: 4.004A pdb=" N TRP A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.630A pdb=" N GLY A 545 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.566A pdb=" N THR A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 632 through 646 Processing helix chain 'A' and resid 648 through 667 removed outlier: 4.046A pdb=" N TRP A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 653 " --> pdb=" O THR A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 90 through 96 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 129 through 140 Proline residue: B 133 - end of helix removed outlier: 4.812A pdb=" N GLN B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.732A pdb=" N LEU B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 256 through 276 Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.591A pdb=" N MET B 367 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 407 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 424 through 453 Processing helix chain 'B' and resid 468 through 487 removed outlier: 3.806A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 511 removed outlier: 4.004A pdb=" N TRP B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 531 Processing helix chain 'B' and resid 533 through 552 removed outlier: 3.630A pdb=" N GLY B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.566A pdb=" N THR B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 632 through 646 Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.047A pdb=" N TRP B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 653 " --> pdb=" O THR B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 90 through 96 Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 129 through 140 Proline residue: C 133 - end of helix removed outlier: 4.811A pdb=" N GLN C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 172 through 180 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.733A pdb=" N LEU C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 256 through 276 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 304 through 310 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.591A pdb=" N MET C 367 " --> pdb=" O ARG C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 407 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 424 through 453 Processing helix chain 'C' and resid 468 through 487 removed outlier: 3.807A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 511 removed outlier: 4.004A pdb=" N TRP C 504 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 531 Processing helix chain 'C' and resid 533 through 552 removed outlier: 3.630A pdb=" N GLY C 545 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.565A pdb=" N THR C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 648 through 667 removed outlier: 4.046A pdb=" N TRP C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 90 through 96 Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 129 through 140 Proline residue: D 133 - end of helix removed outlier: 4.811A pdb=" N GLN D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 172 through 180 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 218 through 225 removed outlier: 3.732A pdb=" N LEU D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 256 through 276 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 304 through 310 Processing helix chain 'D' and resid 351 through 357 Processing helix chain 'D' and resid 364 through 368 removed outlier: 3.590A pdb=" N MET D 367 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 407 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 424 through 453 Processing helix chain 'D' and resid 468 through 487 removed outlier: 3.807A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 511 removed outlier: 4.005A pdb=" N TRP D 504 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 505 " --> pdb=" O VAL D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 531 Processing helix chain 'D' and resid 533 through 552 removed outlier: 3.630A pdb=" N GLY D 545 " --> pdb=" O VAL D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.565A pdb=" N THR D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 632 through 646 Processing helix chain 'D' and resid 648 through 667 removed outlier: 4.047A pdb=" N TRP D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 712 Processing sheet with id= A, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG A 697 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 684 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG B 697 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 684 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG C 697 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 684 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 324 through 326 removed outlier: 3.936A pdb=" N ARG D 697 " --> pdb=" O LEU D 684 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 684 " --> pdb=" O ARG D 697 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2688 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: 5.98 Time building geometry restraints manager: 8.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6248 1.34 - 1.46: 4711 1.46 - 1.58: 9481 1.58 - 1.70: 0 1.70 - 1.81: 160 Bond restraints: 20600 Sorted by residual: bond pdb=" CA GLN C 311 " pdb=" CB GLN C 311 " ideal model delta sigma weight residual 1.526 1.578 -0.051 1.70e-02 3.46e+03 9.17e+00 bond pdb=" CA GLN D 311 " pdb=" CB GLN D 311 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.70e-02 3.46e+03 9.07e+00 bond pdb=" CA GLN A 311 " pdb=" CB GLN A 311 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.70e-02 3.46e+03 9.07e+00 bond pdb=" CA GLN B 311 " pdb=" CB GLN B 311 " ideal model delta sigma weight residual 1.526 1.577 -0.051 1.70e-02 3.46e+03 9.07e+00 bond pdb=" C GLN A 319 " pdb=" N PRO A 320 " ideal model delta sigma weight residual 1.335 1.360 -0.026 1.28e-02 6.10e+03 4.00e+00 ... (remaining 20595 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.57: 503 106.57 - 113.47: 11345 113.47 - 120.36: 7629 120.36 - 127.26: 8243 127.26 - 134.15: 260 Bond angle restraints: 27980 Sorted by residual: angle pdb=" N LEU D 532 " pdb=" CA LEU D 532 " pdb=" C LEU D 532 " ideal model delta sigma weight residual 114.62 107.98 6.64 1.14e+00 7.69e-01 3.39e+01 angle pdb=" N LEU B 532 " pdb=" CA LEU B 532 " pdb=" C LEU B 532 " ideal model delta sigma weight residual 114.62 107.99 6.63 1.14e+00 7.69e-01 3.38e+01 angle pdb=" N LEU A 532 " pdb=" CA LEU A 532 " pdb=" C LEU A 532 " ideal model delta sigma weight residual 114.62 108.02 6.60 1.14e+00 7.69e-01 3.35e+01 angle pdb=" N LEU C 532 " pdb=" CA LEU C 532 " pdb=" C LEU C 532 " ideal model delta sigma weight residual 114.62 108.05 6.57 1.14e+00 7.69e-01 3.32e+01 angle pdb=" N VAL D 343 " pdb=" CA VAL D 343 " pdb=" C VAL D 343 " ideal model delta sigma weight residual 113.71 108.70 5.01 9.50e-01 1.11e+00 2.78e+01 ... (remaining 27975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 10882 16.47 - 32.95: 965 32.95 - 49.42: 156 49.42 - 65.89: 25 65.89 - 82.37: 24 Dihedral angle restraints: 12052 sinusoidal: 4884 harmonic: 7168 Sorted by residual: dihedral pdb=" CA ASP B 531 " pdb=" C ASP B 531 " pdb=" N LEU B 532 " pdb=" CA LEU B 532 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASP C 531 " pdb=" C ASP C 531 " pdb=" N LEU C 532 " pdb=" CA LEU C 532 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASP A 531 " pdb=" C ASP A 531 " pdb=" N LEU A 532 " pdb=" CA LEU A 532 " ideal model delta harmonic sigma weight residual 180.00 156.36 23.64 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 12049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2696 0.057 - 0.113: 448 0.113 - 0.170: 20 0.170 - 0.227: 0 0.227 - 0.283: 12 Chirality restraints: 3176 Sorted by residual: chirality pdb=" C13 CLR D1001 " pdb=" C12 CLR D1001 " pdb=" C14 CLR D1001 " pdb=" C17 CLR D1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C13 CLR C1001 " pdb=" C12 CLR C1001 " pdb=" C14 CLR C1001 " pdb=" C17 CLR C1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C13 CLR B1001 " pdb=" C12 CLR B1001 " pdb=" C14 CLR B1001 " pdb=" C17 CLR B1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3173 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 693 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO D 694 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 694 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 694 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 693 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 694 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 694 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 694 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 693 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.15e+00 pdb=" N PRO C 694 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 694 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 694 " 0.029 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2581 2.76 - 3.29: 20330 3.29 - 3.83: 33705 3.83 - 4.36: 38124 4.36 - 4.90: 65850 Nonbonded interactions: 160590 Sorted by model distance: nonbonded pdb=" OG SER C 461 " pdb=" OD1 ASP C 464 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 461 " pdb=" OD1 ASP B 464 " model vdw 2.220 2.440 nonbonded pdb=" OG SER A 461 " pdb=" OD1 ASP A 464 " model vdw 2.220 2.440 nonbonded pdb=" OG SER D 461 " pdb=" OD1 ASP D 464 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR D 266 " pdb=" OE1 GLU D 283 " model vdw 2.281 2.440 ... (remaining 160585 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' selection = chain 'C' selection = chain 'D' } 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: 1.030 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: 4.940 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 50.210 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.051 20600 Z= 0.203 Angle : 0.743 10.883 27980 Z= 0.436 Chirality : 0.042 0.283 3176 Planarity : 0.004 0.051 3428 Dihedral : 13.011 82.366 7428 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.53 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2432 helix: 1.51 (0.14), residues: 1444 sheet: -0.93 (0.51), residues: 84 loop : -2.64 (0.18), residues: 904 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 342 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 347 average time/residue: 1.3328 time to fit residues: 521.7825 Evaluate side-chains 211 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 217 GLN B 160 HIS B 217 GLN C 160 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS D 217 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20600 Z= 0.272 Angle : 0.607 5.834 27980 Z= 0.305 Chirality : 0.039 0.153 3176 Planarity : 0.004 0.041 3428 Dihedral : 4.860 43.711 2732 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2432 helix: 1.83 (0.14), residues: 1428 sheet: -0.56 (0.51), residues: 84 loop : -2.59 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 222 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 11 residues processed: 252 average time/residue: 1.1249 time to fit residues: 327.1829 Evaluate side-chains 194 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 1 residues processed: 10 average time/residue: 0.2616 time to fit residues: 7.5588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 150 optimal weight: 0.0570 chunk 61 optimal weight: 40.0000 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 197 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 overall best weight: 2.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 20600 Z= 0.252 Angle : 0.561 9.217 27980 Z= 0.284 Chirality : 0.038 0.149 3176 Planarity : 0.004 0.043 3428 Dihedral : 4.654 44.420 2732 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2432 helix: 1.93 (0.14), residues: 1432 sheet: -0.32 (0.52), residues: 84 loop : -2.53 (0.18), residues: 916 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 2.450 Fit side-chains outliers start: 54 outliers final: 18 residues processed: 226 average time/residue: 1.0497 time to fit residues: 277.7038 Evaluate side-chains 196 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 2.395 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 6 residues processed: 12 average time/residue: 0.2739 time to fit residues: 8.4064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 20600 Z= 0.192 Angle : 0.519 5.990 27980 Z= 0.264 Chirality : 0.037 0.165 3176 Planarity : 0.003 0.043 3428 Dihedral : 4.480 46.196 2732 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.17), residues: 2432 helix: 2.01 (0.14), residues: 1436 sheet: -0.19 (0.53), residues: 84 loop : -2.48 (0.18), residues: 912 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 196 time to evaluate : 2.396 Fit side-chains outliers start: 53 outliers final: 23 residues processed: 223 average time/residue: 0.9971 time to fit residues: 262.3994 Evaluate side-chains 195 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 9 residues processed: 14 average time/residue: 0.5789 time to fit residues: 13.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 409 GLN B 409 GLN C 258 ASN C 409 GLN D 258 ASN D 409 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 20600 Z= 0.408 Angle : 0.630 5.829 27980 Z= 0.322 Chirality : 0.041 0.152 3176 Planarity : 0.005 0.045 3428 Dihedral : 4.749 47.519 2732 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.70 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2432 helix: 1.96 (0.14), residues: 1408 sheet: -0.14 (0.56), residues: 84 loop : -2.36 (0.18), residues: 940 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 178 time to evaluate : 2.439 Fit side-chains outliers start: 59 outliers final: 31 residues processed: 218 average time/residue: 1.0080 time to fit residues: 259.3496 Evaluate side-chains 204 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 18 residues processed: 13 average time/residue: 0.2600 time to fit residues: 8.6484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 236 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 409 GLN C 217 GLN C 409 GLN D 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 20600 Z= 0.151 Angle : 0.516 11.765 27980 Z= 0.257 Chirality : 0.037 0.163 3176 Planarity : 0.003 0.044 3428 Dihedral : 4.452 49.046 2732 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2432 helix: 2.15 (0.14), residues: 1420 sheet: -0.02 (0.55), residues: 84 loop : -2.18 (0.18), residues: 928 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 206 time to evaluate : 2.130 Fit side-chains outliers start: 55 outliers final: 19 residues processed: 244 average time/residue: 0.9241 time to fit residues: 269.3571 Evaluate side-chains 200 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 2.345 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.3981 time to fit residues: 5.9934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 134 optimal weight: 0.0770 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS B 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 20600 Z= 0.155 Angle : 0.521 12.192 27980 Z= 0.256 Chirality : 0.036 0.172 3176 Planarity : 0.003 0.041 3428 Dihedral : 4.307 49.843 2732 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2432 helix: 2.27 (0.14), residues: 1420 sheet: 0.10 (0.55), residues: 84 loop : -2.14 (0.18), residues: 928 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.369 Fit side-chains outliers start: 35 outliers final: 9 residues processed: 236 average time/residue: 0.9434 time to fit residues: 265.0580 Evaluate side-chains 195 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 3.2000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 184 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN B 409 GLN C 409 GLN D 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 20600 Z= 0.312 Angle : 0.598 11.666 27980 Z= 0.300 Chirality : 0.039 0.165 3176 Planarity : 0.004 0.041 3428 Dihedral : 4.574 50.561 2732 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.17), residues: 2432 helix: 2.09 (0.14), residues: 1424 sheet: 0.03 (0.55), residues: 84 loop : -2.14 (0.18), residues: 924 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 2.419 Fit side-chains outliers start: 42 outliers final: 18 residues processed: 198 average time/residue: 1.0021 time to fit residues: 234.1223 Evaluate side-chains 182 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 2.407 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.1915 time to fit residues: 5.6402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 95 optimal weight: 0.0030 chunk 172 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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: 0.8239 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20600 Z= 0.156 Angle : 0.528 11.671 27980 Z= 0.259 Chirality : 0.037 0.186 3176 Planarity : 0.003 0.042 3428 Dihedral : 4.388 50.886 2732 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2432 helix: 2.23 (0.14), residues: 1424 sheet: 0.11 (0.54), residues: 84 loop : -2.00 (0.18), residues: 924 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 2.089 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 226 average time/residue: 0.9749 time to fit residues: 260.3049 Evaluate side-chains 197 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 3.2300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 9.9990 chunk 231 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 20600 Z= 0.338 Angle : 0.615 11.647 27980 Z= 0.309 Chirality : 0.040 0.178 3176 Planarity : 0.004 0.042 3428 Dihedral : 4.640 51.142 2732 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2432 helix: 2.04 (0.14), residues: 1428 sheet: 0.09 (0.55), residues: 84 loop : -2.06 (0.18), residues: 920 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 2.356 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 185 average time/residue: 1.0814 time to fit residues: 234.9702 Evaluate side-chains 176 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 2.325 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.1776 time to fit residues: 3.3681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.132118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087511 restraints weight = 35029.751| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.48 r_work: 0.3124 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 20600 Z= 0.232 Angle : 0.559 11.457 27980 Z= 0.279 Chirality : 0.038 0.193 3176 Planarity : 0.004 0.042 3428 Dihedral : 4.556 51.253 2732 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.95 % Favored : 95.89 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2432 helix: 2.11 (0.14), residues: 1428 sheet: 0.16 (0.55), residues: 84 loop : -1.99 (0.19), residues: 920 =============================================================================== Job complete usr+sys time: 6075.98 seconds wall clock time: 109 minutes 23.29 seconds (6563.29 seconds total)