Starting phenix.real_space_refine on Sun Mar 24 06:03:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xev_33160/03_2024/7xev_33160_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xev_33160/03_2024/7xev_33160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xev_33160/03_2024/7xev_33160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xev_33160/03_2024/7xev_33160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xev_33160/03_2024/7xev_33160_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xev_33160/03_2024/7xev_33160_trim_updated.pdb" } resolution = 3.27 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 108 5.16 5 B 4 2.79 5 C 13120 2.51 5 N 3376 2.21 5 O 3440 1.98 5 H 20284 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 609": "OE1" <-> "OE2" Residue "C GLU 703": "OE1" <-> "OE2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D GLU 667": "OE1" <-> "OE2" Residue "D GLU 703": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40332 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "B" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "C" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "D" Number of atoms: 10066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 10066 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 20, 'TRANS': 593} Chain breaks: 2 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'FZ4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.15, per 1000 atoms: 0.43 Number of scatterers: 40332 At special positions: 0 Unit cell: (153.114, 153.114, 118.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 O 3440 8.00 N 3376 7.00 C 13120 6.00 B 4 5.00 H 20284 1.00 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: 30.83 Conformation dependent library (CDL) restraints added in 4.2 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 53.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'A' and resid 72 through 80 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 121 Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.543A pdb=" N LEU A 132 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Proline residue: A 133 - end of helix 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 173 through 180 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 220 through 226 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 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 375 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 486 Processing helix chain 'A' and resid 492 through 511 removed outlier: 4.760A pdb=" N LEU A 508 " --> pdb=" O TRP A 504 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 removed outlier: 3.878A pdb=" N ILE A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 520 " --> pdb=" O HIS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 632 through 646 Processing helix chain 'A' and resid 649 through 667 Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'B' and resid 72 through 80 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 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 130 through 140 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 173 through 180 Processing helix chain 'B' and resid 208 through 214 Processing helix chain 'B' and resid 220 through 226 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 367 Processing helix chain 'B' and resid 375 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 486 Processing helix chain 'B' and resid 492 through 511 removed outlier: 4.772A pdb=" N LEU B 508 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 531 removed outlier: 3.879A pdb=" N ILE B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR B 520 " --> pdb=" O HIS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 552 Processing helix chain 'B' and resid 588 through 600 Processing helix chain 'B' and resid 614 through 628 Processing helix chain 'B' and resid 632 through 646 Processing helix chain 'B' and resid 649 through 667 Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'C' and resid 72 through 80 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 97 Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.573A pdb=" N LEU C 132 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Proline residue: C 133 - end of helix Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 220 through 226 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 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 375 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 486 Processing helix chain 'C' and resid 492 through 511 removed outlier: 4.788A pdb=" N LEU C 508 " --> pdb=" O TRP C 504 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N TYR C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 531 removed outlier: 3.877A pdb=" N ILE C 519 " --> pdb=" O GLN C 515 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR C 520 " --> pdb=" O HIS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 614 through 628 Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 649 through 667 Processing helix chain 'C' and resid 710 through 712 No H-bonds generated for 'chain 'C' and resid 710 through 712' Processing helix chain 'D' and resid 72 through 80 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 121 Processing helix chain 'D' and resid 130 through 140 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 173 through 180 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 220 through 226 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 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 375 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 486 Processing helix chain 'D' and resid 492 through 511 removed outlier: 4.762A pdb=" N LEU D 508 " --> pdb=" O TRP D 504 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR D 510 " --> pdb=" O ASN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 531 removed outlier: 3.878A pdb=" N ILE D 519 " --> pdb=" O GLN D 515 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR D 520 " --> pdb=" O HIS D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'D' and resid 614 through 628 Processing helix chain 'D' and resid 632 through 646 Processing helix chain 'D' and resid 649 through 667 Processing helix chain 'D' and resid 710 through 712 No H-bonds generated for 'chain 'D' and resid 710 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 333 through 339 Processing sheet with id= B, first strand: chain 'B' and resid 333 through 339 removed outlier: 3.659A pdb=" N TYR B 338 " --> pdb=" O PHE B 700 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 333 through 339 removed outlier: 3.656A pdb=" N TYR C 338 " --> pdb=" O PHE C 700 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 333 through 339 removed outlier: 3.656A pdb=" N TYR D 338 " --> pdb=" O PHE D 700 " (cutoff:3.500A) 871 hydrogen bonds defined for protein. 2580 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: 13.58 Time building geometry restraints manager: 32.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20228 1.03 - 1.23: 56 1.23 - 1.42: 8780 1.42 - 1.62: 11616 1.62 - 1.81: 160 Bond restraints: 40840 Sorted by residual: bond pdb=" CB PRO D 372 " pdb=" CG PRO D 372 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.99e+00 bond pdb=" C02 FZ4 C1001 " pdb=" C03 FZ4 C1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C02 FZ4 D1001 " pdb=" C03 FZ4 D1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C02 FZ4 B1001 " pdb=" C03 FZ4 B1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C02 FZ4 A1001 " pdb=" C03 FZ4 A1001 " ideal model delta sigma weight residual 1.400 1.371 0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 40835 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.57: 545 106.57 - 113.47: 47551 113.47 - 120.37: 14063 120.37 - 127.27: 11325 127.27 - 134.17: 272 Bond angle restraints: 73756 Sorted by residual: angle pdb=" N LEU A 373 " pdb=" CA LEU A 373 " pdb=" C LEU A 373 " ideal model delta sigma weight residual 114.12 104.73 9.39 1.39e+00 5.18e-01 4.57e+01 angle pdb=" N LEU B 373 " pdb=" CA LEU B 373 " pdb=" C LEU B 373 " ideal model delta sigma weight residual 114.75 108.91 5.84 1.26e+00 6.30e-01 2.15e+01 angle pdb=" N LEU C 373 " pdb=" CA LEU C 373 " pdb=" C LEU C 373 " ideal model delta sigma weight residual 114.75 109.01 5.74 1.26e+00 6.30e-01 2.07e+01 angle pdb=" N ASN D 374 " pdb=" CA ASN D 374 " pdb=" C ASN D 374 " ideal model delta sigma weight residual 112.72 107.78 4.94 1.28e+00 6.10e-01 1.49e+01 angle pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" CD PRO D 372 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 ... (remaining 73751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.39: 17471 20.39 - 40.78: 1203 40.78 - 61.17: 338 61.17 - 81.56: 23 81.56 - 101.95: 5 Dihedral angle restraints: 19040 sinusoidal: 10212 harmonic: 8828 Sorted by residual: dihedral pdb=" CA PRO A 372 " pdb=" C PRO A 372 " pdb=" N LEU A 373 " pdb=" CA LEU A 373 " ideal model delta harmonic sigma weight residual 180.00 141.39 38.61 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" CA GLU B 371 " pdb=" C GLU B 371 " pdb=" N PRO B 372 " pdb=" CA PRO B 372 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLU C 371 " pdb=" C GLU C 371 " pdb=" N PRO C 372 " pdb=" CA PRO C 372 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 19037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2647 0.048 - 0.096: 434 0.096 - 0.145: 55 0.145 - 0.193: 1 0.193 - 0.241: 3 Chirality restraints: 3140 Sorted by residual: chirality pdb=" CA PRO A 372 " pdb=" N PRO A 372 " pdb=" C PRO A 372 " pdb=" CB PRO A 372 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" C PRO D 372 " pdb=" CB PRO D 372 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA PRO B 372 " pdb=" N PRO B 372 " pdb=" C PRO B 372 " pdb=" CB PRO B 372 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 3137 not shown) Planarity restraints: 5808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 B1001 " -0.443 2.00e-02 2.50e+03 2.82e-01 1.40e+03 pdb=" C02 FZ4 B1001 " 0.247 2.00e-02 2.50e+03 pdb=" C03 FZ4 B1001 " 0.365 2.00e-02 2.50e+03 pdb=" C04 FZ4 B1001 " -0.091 2.00e-02 2.50e+03 pdb=" C05 FZ4 B1001 " -0.306 2.00e-02 2.50e+03 pdb=" C06 FZ4 B1001 " -0.027 2.00e-02 2.50e+03 pdb=" C07 FZ4 B1001 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 C1001 " -0.442 2.00e-02 2.50e+03 2.82e-01 1.39e+03 pdb=" C02 FZ4 C1001 " 0.247 2.00e-02 2.50e+03 pdb=" C03 FZ4 C1001 " 0.364 2.00e-02 2.50e+03 pdb=" C04 FZ4 C1001 " -0.092 2.00e-02 2.50e+03 pdb=" C05 FZ4 C1001 " -0.304 2.00e-02 2.50e+03 pdb=" C06 FZ4 C1001 " -0.028 2.00e-02 2.50e+03 pdb=" C07 FZ4 C1001 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" B01 FZ4 A1001 " 0.434 2.00e-02 2.50e+03 2.77e-01 1.34e+03 pdb=" C02 FZ4 A1001 " -0.244 2.00e-02 2.50e+03 pdb=" C03 FZ4 A1001 " -0.359 2.00e-02 2.50e+03 pdb=" C04 FZ4 A1001 " 0.096 2.00e-02 2.50e+03 pdb=" C05 FZ4 A1001 " 0.293 2.00e-02 2.50e+03 pdb=" C06 FZ4 A1001 " 0.031 2.00e-02 2.50e+03 pdb=" C07 FZ4 A1001 " -0.250 2.00e-02 2.50e+03 ... (remaining 5805 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 2596 2.20 - 2.80: 82890 2.80 - 3.40: 110924 3.40 - 4.00: 139064 4.00 - 4.60: 220027 Nonbonded interactions: 555501 Sorted by model distance: nonbonded pdb=" OE1 GLN C 145 " pdb=" H GLN C 145 " model vdw 1.595 1.850 nonbonded pdb=" OE1 GLN B 145 " pdb=" H GLN B 145 " model vdw 1.618 1.850 nonbonded pdb=" OE1 GLN A 145 " pdb=" H GLN A 145 " model vdw 1.624 1.850 nonbonded pdb=" OH TYR B 539 " pdb=" HG1 THR B 599 " model vdw 1.624 1.850 nonbonded pdb=" OE1 GLN D 145 " pdb=" H GLN D 145 " model vdw 1.627 1.850 ... (remaining 555496 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: 0.400 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: 0.590 Extract box with map and model: 4.670 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 121.790 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 0.086 20556 Z= 0.166 Angle : 0.536 10.574 27884 Z= 0.289 Chirality : 0.036 0.241 3140 Planarity : 0.014 0.282 3440 Dihedral : 14.964 101.945 7424 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 2432 helix: 2.01 (0.15), residues: 1448 sheet: -3.57 (0.48), residues: 84 loop : -1.84 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 173 HIS 0.004 0.001 HIS D 516 PHE 0.010 0.001 PHE C 76 TYR 0.020 0.001 TYR A 539 ARG 0.007 0.000 ARG D 188 *********************** 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 267 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 539 TYR cc_start: 0.7757 (t80) cc_final: 0.7404 (t80) REVERT: D 539 TYR cc_start: 0.7466 (t80) cc_final: 0.7153 (t80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.6941 time to fit residues: 286.0908 Evaluate side-chains 213 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.510 ------------------------------------------------------------------------------- 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: 5.9990 chunk 184 optimal weight: 20.0000 chunk 102 optimal weight: 0.3980 chunk 63 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20556 Z= 0.313 Angle : 0.560 6.498 27884 Z= 0.295 Chirality : 0.036 0.237 3140 Planarity : 0.006 0.127 3440 Dihedral : 6.219 76.723 2720 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.29 % Favored : 93.54 % Rotamer: Outliers : 1.01 % Allowed : 4.92 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % 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: 0.30 (0.18), residues: 2432 helix: 1.63 (0.14), residues: 1452 sheet: -3.79 (0.46), residues: 88 loop : -1.84 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 173 HIS 0.004 0.001 HIS A 408 PHE 0.008 0.001 PHE D 392 TYR 0.027 0.002 TYR B 338 ARG 0.004 0.000 ARG B 170 *********************** 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 237 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 215 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.5851 (m-80) cc_final: 0.5368 (m-80) REVERT: D 539 TYR cc_start: 0.7975 (t80) cc_final: 0.7637 (t80) outliers start: 22 outliers final: 17 residues processed: 237 average time/residue: 0.6751 time to fit residues: 250.6160 Evaluate side-chains 227 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 184 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 221 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 178 optimal weight: 0.1980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20556 Z= 0.216 Angle : 0.507 9.862 27884 Z= 0.264 Chirality : 0.035 0.254 3140 Planarity : 0.005 0.132 3440 Dihedral : 6.232 81.657 2720 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 0.83 % Allowed : 7.67 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % 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: 0.44 (0.18), residues: 2432 helix: 1.75 (0.14), residues: 1452 sheet: -3.63 (0.48), residues: 88 loop : -1.83 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 655 HIS 0.003 0.001 HIS B 516 PHE 0.008 0.001 PHE C 462 TYR 0.019 0.001 TYR B 338 ARG 0.002 0.000 ARG A 614 *********************** 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 230 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 3.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 TYR cc_start: 0.7886 (t80) cc_final: 0.7652 (t80) REVERT: B 70 PHE cc_start: 0.5872 (m-80) cc_final: 0.5360 (m-80) REVERT: B 539 TYR cc_start: 0.7964 (t80) cc_final: 0.7729 (t80) REVERT: D 539 TYR cc_start: 0.7867 (t80) cc_final: 0.7421 (t80) outliers start: 18 outliers final: 17 residues processed: 229 average time/residue: 0.6765 time to fit residues: 243.1410 Evaluate side-chains 222 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain B residue 173 TRP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR 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: 1.9990 chunk 115 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 63 optimal weight: 30.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20556 Z= 0.198 Angle : 0.484 6.005 27884 Z= 0.255 Chirality : 0.034 0.232 3140 Planarity : 0.005 0.121 3440 Dihedral : 6.108 83.870 2720 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 1.24 % Allowed : 9.01 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % 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 (0.18), residues: 2432 helix: 1.82 (0.14), residues: 1456 sheet: -3.53 (0.50), residues: 88 loop : -1.78 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 655 HIS 0.003 0.001 HIS B 516 PHE 0.007 0.001 PHE A 76 TYR 0.019 0.001 TYR B 338 ARG 0.002 0.000 ARG C 139 *********************** 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 233 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 TYR cc_start: 0.7839 (t80) cc_final: 0.7628 (t80) REVERT: B 70 PHE cc_start: 0.5865 (m-80) cc_final: 0.5322 (m-80) REVERT: B 539 TYR cc_start: 0.7925 (t80) cc_final: 0.7661 (t80) REVERT: C 539 TYR cc_start: 0.8002 (t80) cc_final: 0.7745 (t80) REVERT: D 539 TYR cc_start: 0.7889 (t80) cc_final: 0.7585 (t80) REVERT: D 703 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7358 (mp0) outliers start: 27 outliers final: 26 residues processed: 232 average time/residue: 0.6735 time to fit residues: 245.9968 Evaluate side-chains 227 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20556 Z= 0.386 Angle : 0.585 6.507 27884 Z= 0.311 Chirality : 0.037 0.224 3140 Planarity : 0.006 0.126 3440 Dihedral : 6.539 85.598 2720 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.03 % Favored : 92.80 % Rotamer: Outliers : 1.79 % Allowed : 10.25 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % Twisted General : 0.04 % 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: -0.06 (0.18), residues: 2432 helix: 1.33 (0.14), residues: 1448 sheet: -3.90 (0.46), residues: 88 loop : -1.99 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 328 HIS 0.005 0.001 HIS A 408 PHE 0.009 0.002 PHE B 392 TYR 0.028 0.002 TYR B 338 ARG 0.003 0.000 ARG B 555 *********************** 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: 39 poor density : 198 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6018 (m-80) cc_final: 0.5568 (m-80) REVERT: C 139 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7844 (tpp-160) REVERT: D 70 PHE cc_start: 0.5397 (m-80) cc_final: 0.5053 (m-80) REVERT: D 703 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7382 (mp0) outliers start: 39 outliers final: 34 residues processed: 234 average time/residue: 0.6634 time to fit residues: 245.6292 Evaluate side-chains 231 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 236 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 109 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20556 Z= 0.220 Angle : 0.503 5.933 27884 Z= 0.266 Chirality : 0.035 0.217 3140 Planarity : 0.005 0.122 3440 Dihedral : 6.289 86.795 2720 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 1.75 % Allowed : 11.17 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.25 (0.18), residues: 2432 helix: 1.58 (0.14), residues: 1452 sheet: -3.76 (0.48), residues: 88 loop : -1.86 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 655 HIS 0.003 0.001 HIS C 516 PHE 0.008 0.001 PHE A 596 TYR 0.022 0.001 TYR A 338 ARG 0.002 0.000 ARG A 614 *********************** 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 241 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.6026 (m-80) cc_final: 0.5504 (m-80) REVERT: C 139 ARG cc_start: 0.8132 (ptt90) cc_final: 0.7890 (tpp-160) REVERT: C 539 TYR cc_start: 0.8025 (t80) cc_final: 0.7737 (t80) REVERT: D 70 PHE cc_start: 0.5388 (m-80) cc_final: 0.4885 (m-80) REVERT: D 703 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7389 (mp0) outliers start: 38 outliers final: 37 residues processed: 236 average time/residue: 0.6637 time to fit residues: 247.9848 Evaluate side-chains 240 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 147 optimal weight: 0.0050 chunk 143 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 overall best weight: 3.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20556 Z= 0.224 Angle : 0.499 5.669 27884 Z= 0.264 Chirality : 0.035 0.209 3140 Planarity : 0.005 0.121 3440 Dihedral : 6.187 86.532 2720 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 1.84 % Allowed : 11.76 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.34 (0.18), residues: 2432 helix: 1.66 (0.14), residues: 1452 sheet: -3.75 (0.48), residues: 88 loop : -1.84 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 655 HIS 0.003 0.001 HIS A 408 PHE 0.008 0.001 PHE A 76 TYR 0.023 0.001 TYR A 338 ARG 0.002 0.000 ARG C 512 *********************** 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 251 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 211 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.5700 (m-80) cc_final: 0.5239 (m-80) REVERT: C 139 ARG cc_start: 0.8143 (ptt90) cc_final: 0.7905 (tpp-160) REVERT: C 511 THR cc_start: 0.6231 (OUTLIER) cc_final: 0.5982 (t) REVERT: C 539 TYR cc_start: 0.8034 (t80) cc_final: 0.7715 (t80) REVERT: D 70 PHE cc_start: 0.5392 (m-80) cc_final: 0.4942 (m-80) REVERT: D 539 TYR cc_start: 0.7969 (t80) cc_final: 0.7747 (t80) REVERT: D 703 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7404 (mp0) outliers start: 40 outliers final: 37 residues processed: 244 average time/residue: 0.6914 time to fit residues: 262.6109 Evaluate side-chains 241 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20556 Z= 0.289 Angle : 0.537 5.768 27884 Z= 0.284 Chirality : 0.036 0.203 3140 Planarity : 0.005 0.123 3440 Dihedral : 6.293 85.734 2720 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.33 % Favored : 93.50 % Rotamer: Outliers : 1.98 % Allowed : 12.73 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.13 (0.18), residues: 2432 helix: 1.49 (0.14), residues: 1444 sheet: -3.65 (0.50), residues: 84 loop : -1.92 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 328 HIS 0.004 0.001 HIS D 408 PHE 0.008 0.001 PHE B 544 TYR 0.024 0.002 TYR A 338 ARG 0.005 0.000 ARG C 74 *********************** 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 243 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 PHE cc_start: 0.5811 (m-80) cc_final: 0.5382 (m-80) REVERT: B 511 THR cc_start: 0.6290 (OUTLIER) cc_final: 0.6044 (t) REVERT: C 539 TYR cc_start: 0.8139 (t80) cc_final: 0.7928 (t80) REVERT: D 70 PHE cc_start: 0.5548 (m-80) cc_final: 0.5121 (m-80) REVERT: D 511 THR cc_start: 0.6284 (OUTLIER) cc_final: 0.6041 (t) REVERT: D 539 TYR cc_start: 0.8081 (t80) cc_final: 0.7881 (t80) REVERT: D 703 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7367 (mp0) outliers start: 43 outliers final: 38 residues processed: 235 average time/residue: 0.6283 time to fit residues: 233.9121 Evaluate side-chains 240 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 7.9990 chunk 225 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 218 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20556 Z= 0.239 Angle : 0.515 5.913 27884 Z= 0.272 Chirality : 0.035 0.201 3140 Planarity : 0.005 0.121 3440 Dihedral : 6.215 86.498 2720 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 1.88 % Allowed : 13.14 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.25 (0.18), residues: 2432 helix: 1.58 (0.14), residues: 1444 sheet: -3.53 (0.51), residues: 84 loop : -1.88 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 655 HIS 0.003 0.001 HIS B 408 PHE 0.007 0.001 PHE D 596 TYR 0.023 0.001 TYR A 338 ARG 0.004 0.000 ARG C 74 *********************** 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 242 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 THR cc_start: 0.6277 (OUTLIER) cc_final: 0.6040 (t) REVERT: B 70 PHE cc_start: 0.5805 (m-80) cc_final: 0.5347 (m-80) REVERT: B 511 THR cc_start: 0.6194 (OUTLIER) cc_final: 0.5979 (t) REVERT: C 539 TYR cc_start: 0.8068 (t80) cc_final: 0.7823 (t80) REVERT: D 70 PHE cc_start: 0.5558 (m-80) cc_final: 0.5114 (m-80) REVERT: D 511 THR cc_start: 0.6214 (OUTLIER) cc_final: 0.5995 (t) REVERT: D 539 TYR cc_start: 0.8002 (t80) cc_final: 0.7766 (t80) REVERT: D 703 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7406 (mp0) outliers start: 41 outliers final: 35 residues processed: 234 average time/residue: 0.6831 time to fit residues: 254.8239 Evaluate side-chains 239 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Chi-restraints excluded: chain D residue 703 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0970 chunk 231 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20556 Z= 0.159 Angle : 0.479 5.373 27884 Z= 0.250 Chirality : 0.034 0.200 3140 Planarity : 0.005 0.118 3440 Dihedral : 5.966 87.148 2720 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.80 % Favored : 94.04 % Rotamer: Outliers : 1.61 % Allowed : 13.47 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.59 (0.18), residues: 2432 helix: 1.96 (0.15), residues: 1420 sheet: -3.33 (0.53), residues: 84 loop : -1.83 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 655 HIS 0.003 0.001 HIS B 516 PHE 0.007 0.001 PHE C 76 TYR 0.019 0.001 TYR A 338 ARG 0.003 0.000 ARG C 512 ********************** 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 243 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 THR cc_start: 0.6014 (OUTLIER) cc_final: 0.5791 (t) REVERT: B 70 PHE cc_start: 0.5752 (m-80) cc_final: 0.5288 (m-80) REVERT: D 70 PHE cc_start: 0.5516 (m-80) cc_final: 0.5061 (m-80) outliers start: 35 outliers final: 31 residues processed: 237 average time/residue: 0.7306 time to fit residues: 273.4660 Evaluate side-chains 237 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 3.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 552 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.153163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.116050 restraints weight = 104362.426| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.15 r_work: 0.3610 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20556 Z= 0.235 Angle : 0.510 5.545 27884 Z= 0.268 Chirality : 0.035 0.199 3140 Planarity : 0.005 0.119 3440 Dihedral : 6.004 83.448 2720 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.13 % Favored : 93.71 % Rotamer: Outliers : 1.61 % Allowed : 13.51 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.95 % 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: 0.45 (0.18), residues: 2432 helix: 1.83 (0.14), residues: 1420 sheet: -3.40 (0.53), residues: 84 loop : -1.87 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 655 HIS 0.003 0.001 HIS D 408 PHE 0.014 0.001 PHE C 76 TYR 0.030 0.002 TYR A 492 ARG 0.003 0.000 ARG C 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7250.80 seconds wall clock time: 131 minutes 30.00 seconds (7890.00 seconds total)