Starting phenix.real_space_refine on Sat Feb 17 22:51:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/02_2024/7xer_33158_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/02_2024/7xer_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_33158/02_2024/7xer_33158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/02_2024/7xer_33158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/02_2024/7xer_33158_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xer_33158/02_2024/7xer_33158_updated.pdb" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.41, per 1000 atoms: 0.52 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: 7.21 Conformation dependent library (CDL) restraints added in 3.7 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: 4.75 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: 5.93 Time building geometry restraints manager: 7.92 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: 11070 16.47 - 32.95: 993 32.95 - 49.42: 156 49.42 - 65.89: 33 65.89 - 82.37: 24 Dihedral angle restraints: 12276 sinusoidal: 5108 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 12273 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: 0.800 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: 4.340 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 52.670 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.130 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:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.460 ------------------------------------------------------------------------------- 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 : 13.071 82.366 7652 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 % Allowed : 0.64 % Favored : 99.13 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 218 HIS 0.002 0.001 HIS B 160 PHE 0.019 0.001 PHE A 467 TYR 0.023 0.002 TYR D 157 ARG 0.004 0.000 ARG C 512 *********************** 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 : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 685 LYS cc_start: 0.8555 (tttp) cc_final: 0.8352 (tptt) outliers start: 5 outliers final: 0 residues processed: 347 average time/residue: 1.2904 time to fit residues: 504.9827 Evaluate side-chains 212 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 A 258 ASN B 160 HIS B 217 GLN B 258 ASN C 160 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN D 160 HIS D 217 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20600 Z= 0.265 Angle : 0.612 6.129 27980 Z= 0.308 Chirality : 0.039 0.183 3176 Planarity : 0.004 0.046 3428 Dihedral : 5.718 57.417 2956 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 2.76 % Allowed : 11.12 % Favored : 86.12 % 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: 0.26 (0.17), residues: 2432 helix: 1.82 (0.14), residues: 1424 sheet: -0.58 (0.51), residues: 84 loop : -2.58 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 173 HIS 0.007 0.001 HIS C 229 PHE 0.024 0.002 PHE D 486 TYR 0.013 0.002 TYR D 466 ARG 0.009 0.001 ARG C 158 *********************** 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 281 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 221 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 192 ARG cc_start: 0.6970 (tpm170) cc_final: 0.6581 (tpp-160) REVERT: C 483 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8860 (t) REVERT: C 602 MET cc_start: 0.9169 (mmm) cc_final: 0.8816 (mmm) REVERT: D 434 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (mp) REVERT: D 602 MET cc_start: 0.9071 (mmm) cc_final: 0.8744 (mmp) outliers start: 60 outliers final: 13 residues processed: 253 average time/residue: 1.1576 time to fit residues: 336.2867 Evaluate side-chains 196 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 61 optimal weight: 40.0000 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 258 ASN D 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20600 Z= 0.374 Angle : 0.629 5.724 27980 Z= 0.322 Chirality : 0.041 0.149 3176 Planarity : 0.005 0.047 3428 Dihedral : 5.459 50.775 2956 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.85 % Favored : 94.98 % Rotamer: Outliers : 2.44 % Allowed : 16.22 % Favored : 81.34 % 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: 0.35 (0.17), residues: 2432 helix: 1.90 (0.14), residues: 1408 sheet: -0.45 (0.53), residues: 84 loop : -2.48 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 173 HIS 0.006 0.001 HIS C 229 PHE 0.017 0.002 PHE D 402 TYR 0.017 0.002 TYR C 466 ARG 0.007 0.001 ARG C 307 *********************** 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 238 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 185 time to evaluate : 2.429 Fit side-chains REVERT: A 168 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6827 (tm-30) REVERT: B 168 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: C 192 ARG cc_start: 0.6927 (tpm170) cc_final: 0.6694 (tpp-160) REVERT: C 250 MET cc_start: 0.8641 (mmt) cc_final: 0.8435 (mmt) REVERT: C 483 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8959 (t) REVERT: C 602 MET cc_start: 0.9143 (mmm) cc_final: 0.8705 (mmp) REVERT: D 168 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6837 (tm-30) outliers start: 53 outliers final: 19 residues processed: 214 average time/residue: 1.0387 time to fit residues: 259.6554 Evaluate side-chains 193 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 483 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8228 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20600 Z= 0.158 Angle : 0.507 8.818 27980 Z= 0.259 Chirality : 0.037 0.165 3176 Planarity : 0.003 0.044 3428 Dihedral : 5.061 48.698 2956 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.62 % Favored : 96.26 % Rotamer: Outliers : 2.53 % Allowed : 17.60 % Favored : 79.87 % 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: 0.66 (0.17), residues: 2432 helix: 2.11 (0.14), residues: 1412 sheet: -0.25 (0.53), residues: 84 loop : -2.31 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 173 HIS 0.004 0.001 HIS C 229 PHE 0.010 0.001 PHE C 486 TYR 0.019 0.001 TYR B 466 ARG 0.004 0.000 ARG D 454 *********************** 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 254 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 199 time to evaluate : 2.211 Fit side-chains REVERT: A 168 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: A 602 MET cc_start: 0.9032 (mmm) cc_final: 0.8648 (mmp) REVERT: B 168 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: C 168 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: C 192 ARG cc_start: 0.7035 (tpm170) cc_final: 0.6775 (tpp-160) REVERT: C 250 MET cc_start: 0.8599 (mmt) cc_final: 0.8381 (mmm) REVERT: D 168 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6655 (tm-30) outliers start: 55 outliers final: 17 residues processed: 231 average time/residue: 0.9916 time to fit residues: 268.7895 Evaluate side-chains 196 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 666 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 120 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN C 409 GLN D 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20600 Z= 0.334 Angle : 0.585 9.119 27980 Z= 0.299 Chirality : 0.040 0.161 3176 Planarity : 0.004 0.044 3428 Dihedral : 5.070 48.014 2956 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.94 % Rotamer: Outliers : 3.40 % Allowed : 18.01 % Favored : 78.58 % 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: 0.58 (0.17), residues: 2432 helix: 2.01 (0.14), residues: 1416 sheet: -0.12 (0.55), residues: 84 loop : -2.32 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 173 HIS 0.004 0.001 HIS C 308 PHE 0.017 0.001 PHE C 389 TYR 0.022 0.002 TYR B 466 ARG 0.004 0.001 ARG A 307 *********************** 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 255 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 181 time to evaluate : 2.486 Fit side-chains REVERT: A 168 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: A 602 MET cc_start: 0.9048 (mmm) cc_final: 0.8662 (mmp) REVERT: B 168 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: C 168 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: C 192 ARG cc_start: 0.6998 (tpm170) cc_final: 0.6792 (tpp-160) REVERT: C 250 MET cc_start: 0.8613 (mmt) cc_final: 0.8413 (mmt) REVERT: C 678 HIS cc_start: 0.7197 (t-90) cc_final: 0.6692 (t-90) REVERT: D 168 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6712 (tm-30) outliers start: 74 outliers final: 39 residues processed: 220 average time/residue: 0.9805 time to fit residues: 254.1510 Evaluate side-chains 214 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 20600 Z= 0.333 Angle : 0.598 9.495 27980 Z= 0.303 Chirality : 0.040 0.203 3176 Planarity : 0.004 0.046 3428 Dihedral : 5.047 50.191 2956 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 3.35 % Allowed : 18.34 % Favored : 78.31 % 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: 0.58 (0.17), residues: 2432 helix: 1.96 (0.14), residues: 1416 sheet: 0.01 (0.56), residues: 84 loop : -2.23 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 173 HIS 0.004 0.001 HIS C 229 PHE 0.017 0.001 PHE C 486 TYR 0.019 0.002 TYR B 466 ARG 0.005 0.001 ARG D 307 *********************** 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 245 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 172 time to evaluate : 2.119 Fit side-chains REVERT: A 168 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: A 602 MET cc_start: 0.9062 (mmm) cc_final: 0.8740 (mmp) REVERT: B 168 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6740 (tm-30) REVERT: D 168 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6842 (tm-30) outliers start: 73 outliers final: 40 residues processed: 225 average time/residue: 1.0116 time to fit residues: 266.4086 Evaluate side-chains 208 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 0.0050 chunk 108 optimal weight: 0.9980 overall best weight: 1.1398 ------------------------------------------------------------------------------- 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 229 HIS C 409 GLN D 409 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2869 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= 0.165 Angle : 0.520 12.575 27980 Z= 0.258 Chirality : 0.037 0.168 3176 Planarity : 0.003 0.045 3428 Dihedral : 4.782 51.660 2956 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.85 % Rotamer: Outliers : 2.80 % Allowed : 19.62 % Favored : 77.57 % 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: 0.86 (0.17), residues: 2432 helix: 2.20 (0.14), residues: 1420 sheet: 0.05 (0.56), residues: 84 loop : -2.14 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 173 HIS 0.003 0.001 HIS C 229 PHE 0.017 0.001 PHE C 486 TYR 0.018 0.001 TYR B 466 ARG 0.003 0.000 ARG D 454 *********************** 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 253 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 192 time to evaluate : 2.461 Fit side-chains REVERT: A 201 CYS cc_start: 0.6374 (p) cc_final: 0.6022 (p) REVERT: A 321 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8405 (pp) REVERT: A 602 MET cc_start: 0.9037 (mmm) cc_final: 0.8672 (mmp) REVERT: B 168 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: B 321 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8488 (pp) REVERT: C 168 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: C 230 GLN cc_start: 0.7480 (pt0) cc_final: 0.7236 (pt0) REVERT: C 250 MET cc_start: 0.8593 (mmt) cc_final: 0.8379 (mmm) REVERT: C 321 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8405 (pp) REVERT: C 678 HIS cc_start: 0.7151 (t-90) cc_final: 0.6713 (t-90) REVERT: D 321 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8439 (pp) outliers start: 61 outliers final: 28 residues processed: 235 average time/residue: 1.0193 time to fit residues: 283.6414 Evaluate side-chains 209 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 492 TYR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 492 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 TYR Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 0.2980 chunk 184 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20600 Z= 0.143 Angle : 0.519 13.591 27980 Z= 0.254 Chirality : 0.037 0.372 3176 Planarity : 0.003 0.042 3428 Dihedral : 4.625 52.406 2956 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.02 % Allowed : 20.54 % Favored : 77.44 % 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: 1.08 (0.17), residues: 2432 helix: 2.36 (0.14), residues: 1416 sheet: 0.16 (0.54), residues: 84 loop : -2.01 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 218 HIS 0.003 0.001 HIS C 186 PHE 0.018 0.001 PHE C 486 TYR 0.025 0.001 TYR A 466 ARG 0.002 0.000 ARG A 170 *********************** 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 259 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 215 time to evaluate : 2.335 Fit side-chains REVERT: A 602 MET cc_start: 0.9021 (mmm) cc_final: 0.8715 (mmp) REVERT: C 113 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.6150 (tmtm) REVERT: C 230 GLN cc_start: 0.7492 (pt0) cc_final: 0.7253 (pt0) REVERT: C 250 MET cc_start: 0.8564 (mmt) cc_final: 0.8340 (mmm) REVERT: C 678 HIS cc_start: 0.7166 (t-90) cc_final: 0.6743 (t-90) outliers start: 44 outliers final: 19 residues processed: 247 average time/residue: 0.9189 time to fit residues: 269.3205 Evaluate side-chains 199 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.0570 chunk 225 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 172 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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: 0.8213 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20600 Z= 0.140 Angle : 0.530 13.368 27980 Z= 0.254 Chirality : 0.037 0.324 3176 Planarity : 0.003 0.046 3428 Dihedral : 4.535 53.654 2956 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.33 % Allowed : 21.42 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2432 helix: 2.42 (0.14), residues: 1424 sheet: 0.29 (0.54), residues: 84 loop : -1.98 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 218 HIS 0.002 0.001 HIS C 164 PHE 0.018 0.001 PHE C 486 TYR 0.029 0.001 TYR A 466 ARG 0.003 0.000 ARG D 454 *********************** 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: 29 poor density : 199 time to evaluate : 2.359 Fit side-chains REVERT: A 602 MET cc_start: 0.9001 (mmm) cc_final: 0.8776 (mmp) REVERT: C 168 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6859 (tm-30) REVERT: C 230 GLN cc_start: 0.7487 (pt0) cc_final: 0.7282 (pt0) outliers start: 29 outliers final: 9 residues processed: 221 average time/residue: 0.9322 time to fit residues: 244.6696 Evaluate side-chains 193 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.8372 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 20600 Z= 0.539 Angle : 0.728 15.386 27980 Z= 0.365 Chirality : 0.045 0.352 3176 Planarity : 0.006 0.061 3428 Dihedral : 5.158 50.701 2956 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 1.65 % Allowed : 21.69 % Favored : 76.65 % 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: 0.55 (0.17), residues: 2432 helix: 1.91 (0.14), residues: 1412 sheet: 0.21 (0.57), residues: 84 loop : -2.20 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 218 HIS 0.004 0.002 HIS C 408 PHE 0.020 0.002 PHE C 486 TYR 0.027 0.003 TYR D 510 ARG 0.006 0.001 ARG C 364 ********************** 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 197 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 2.287 Fit side-chains REVERT: A 296 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8820 (tt) REVERT: A 602 MET cc_start: 0.9084 (mmm) cc_final: 0.8738 (mmp) REVERT: A 666 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8566 (mtm) REVERT: B 296 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8815 (tt) REVERT: B 666 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8549 (mtm) REVERT: C 168 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6813 (tm-30) REVERT: C 230 GLN cc_start: 0.7264 (pt0) cc_final: 0.7007 (pt0) REVERT: C 296 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8820 (tt) REVERT: C 602 MET cc_start: 0.9076 (mmm) cc_final: 0.8839 (mmp) REVERT: C 666 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8569 (mtm) REVERT: C 678 HIS cc_start: 0.7175 (t-90) cc_final: 0.6885 (t-90) REVERT: D 296 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8820 (tt) REVERT: D 666 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8549 (mtm) outliers start: 36 outliers final: 18 residues processed: 185 average time/residue: 1.0477 time to fit residues: 228.8982 Evaluate side-chains 181 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 MET Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 MET Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 178 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 193 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6156 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.133814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.089692 restraints weight = 35059.134| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.69 r_work: 0.3145 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20600 Z= 0.162 Angle : 0.553 13.688 27980 Z= 0.270 Chirality : 0.038 0.352 3176 Planarity : 0.004 0.049 3428 Dihedral : 4.863 53.100 2956 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.97 % Allowed : 22.52 % Favored : 76.52 % 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: 1.01 (0.17), residues: 2432 helix: 2.25 (0.14), residues: 1416 sheet: 0.37 (0.56), residues: 84 loop : -1.94 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 218 HIS 0.003 0.001 HIS D 164 PHE 0.018 0.001 PHE C 486 TYR 0.018 0.001 TYR A 466 ARG 0.003 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.52 seconds wall clock time: 116 minutes 37.64 seconds (6997.64 seconds total)