Starting phenix.real_space_refine on Fri Aug 9 09:23:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrr_34065/08_2024/7yrr_34065.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrr_34065/08_2024/7yrr_34065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrr_34065/08_2024/7yrr_34065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrr_34065/08_2024/7yrr_34065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrr_34065/08_2024/7yrr_34065.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yrr_34065/08_2024/7yrr_34065.cif" } resolution = 4.3 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 796 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 114 5.16 5 C 8520 2.51 5 N 2330 2.21 5 O 2565 1.98 5 H 11408 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 1": "OE1" <-> "OE2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 799": "OE1" <-> "OE2" Residue "B ASP 803": "OD1" <-> "OD2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B GLU 844": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24937 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 12029 Classifications: {'peptide': 799} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 47, 'TRANS': 751} Chain breaks: 20 Chain: "B" Number of atoms: 12242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 12242 Classifications: {'peptide': 810} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 47, 'TRANS': 762} Chain breaks: 13 Chain: "C" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Chain: "D" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 333 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Time building chain proxies: 10.88, per 1000 atoms: 0.44 Number of scatterers: 24937 At special positions: 0 Unit cell: (96.759, 127.358, 139.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 O 2565 8.00 N 2330 7.00 C 8520 6.00 H 11408 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.06 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.01 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.07 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.05 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.02 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.02 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.02 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.02 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.01 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=1.99 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.02 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 323 " distance=2.02 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.02 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.02 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.04 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.02 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.02 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.93 Conformation dependent library (CDL) restraints added in 2.5 seconds 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 27 sheets defined 15.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.625A pdb=" N LYS A 17 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.325A pdb=" N ASP A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.736A pdb=" N LEU A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.492A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.526A pdb=" N TYR A 388 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.700A pdb=" N MET A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 removed outlier: 3.716A pdb=" N GLY A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 678 through 698 removed outlier: 4.246A pdb=" N GLU A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 688 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.609A pdb=" N LYS B 17 " --> pdb=" O GLN B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.940A pdb=" N GLY B 149 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.925A pdb=" N CYS B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 320 removed outlier: 4.247A pdb=" N LEU B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.113A pdb=" N PHE B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 372 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.799A pdb=" N GLU B 428 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 429 " --> pdb=" O VAL B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 512 through 516 removed outlier: 3.689A pdb=" N GLY B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 668 through 672 removed outlier: 4.171A pdb=" N ALA B 671 " --> pdb=" O PRO B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 4.446A pdb=" N TYR B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.614A pdb=" N VAL C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.571A pdb=" N TYR D 60 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 8 removed outlier: 6.722A pdb=" N ILE A 7 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.719A pdb=" N GLU A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 231 removed outlier: 5.880A pdb=" N TYR A 225 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ASP A 248 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA6, first strand: chain 'A' and resid 392 through 393 removed outlier: 6.336A pdb=" N VAL A 392 " --> pdb=" O ALA A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 465 through 467 removed outlier: 4.055A pdb=" N SER A 467 " --> pdb=" O THR A 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.534A pdb=" N LYS A 600 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 614 through 618 Processing sheet with id=AB1, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.540A pdb=" N ALA A 793 " --> pdb=" O TYR A 769 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 812 through 813 Processing sheet with id=AB3, first strand: chain 'A' and resid 846 through 851 Processing sheet with id=AB4, first strand: chain 'A' and resid 869 through 870 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 30 removed outlier: 6.439A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 85 through 88 removed outlier: 7.789A pdb=" N ARG B 112 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.572A pdb=" N GLU B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 230 through 231 Processing sheet with id=AB9, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AC1, first strand: chain 'B' and resid 310 through 311 Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 392 through 393 removed outlier: 6.322A pdb=" N VAL B 392 " --> pdb=" O ALA B 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AC5, first strand: chain 'B' and resid 587 through 590 Processing sheet with id=AC6, first strand: chain 'B' and resid 747 through 752 removed outlier: 3.600A pdb=" N SER B 750 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AC8, first strand: chain 'B' and resid 834 through 838 Processing sheet with id=AC9, first strand: chain 'B' and resid 869 through 870 189 hydrogen bonds defined for protein. 417 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: 8.78 Time building geometry restraints manager: 21.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11408 1.03 - 1.23: 252 1.23 - 1.43: 5641 1.43 - 1.62: 7782 1.62 - 1.82: 144 Bond restraints: 25227 Sorted by residual: bond pdb=" C PRO A 543 " pdb=" O PRO A 543 " ideal model delta sigma weight residual 1.233 1.155 0.078 1.13e-02 7.83e+03 4.73e+01 bond pdb=" C PRO B 144 " pdb=" O PRO B 144 " ideal model delta sigma weight residual 1.240 1.173 0.067 1.12e-02 7.97e+03 3.63e+01 bond pdb=" C VAL B 426 " pdb=" O VAL B 426 " ideal model delta sigma weight residual 1.241 1.171 0.070 1.19e-02 7.06e+03 3.44e+01 bond pdb=" N ARG B 455 " pdb=" CA ARG B 455 " ideal model delta sigma weight residual 1.457 1.490 -0.033 6.40e-03 2.44e+04 2.67e+01 bond pdb=" C ILE B 615 " pdb=" O ILE B 615 " ideal model delta sigma weight residual 1.236 1.186 0.050 9.80e-03 1.04e+04 2.58e+01 ... (remaining 25222 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.82: 368 104.82 - 112.37: 26115 112.37 - 119.92: 9912 119.92 - 127.47: 8057 127.47 - 135.02: 147 Bond angle restraints: 44599 Sorted by residual: angle pdb=" N PRO A 603 " pdb=" CA PRO A 603 " pdb=" C PRO A 603 " ideal model delta sigma weight residual 110.70 100.10 10.60 1.22e+00 6.72e-01 7.55e+01 angle pdb=" N PRO B 144 " pdb=" CA PRO B 144 " pdb=" C PRO B 144 " ideal model delta sigma weight residual 110.70 120.47 -9.77 1.22e+00 6.72e-01 6.42e+01 angle pdb=" N ASN B 694 " pdb=" CA ASN B 694 " pdb=" C ASN B 694 " ideal model delta sigma weight residual 112.94 102.31 10.63 1.41e+00 5.03e-01 5.69e+01 angle pdb=" N PHE B 692 " pdb=" CA PHE B 692 " pdb=" C PHE B 692 " ideal model delta sigma weight residual 113.23 104.26 8.97 1.24e+00 6.50e-01 5.23e+01 angle pdb=" N ILE B 106 " pdb=" CA ILE B 106 " pdb=" C ILE B 106 " ideal model delta sigma weight residual 112.43 105.88 6.55 9.20e-01 1.18e+00 5.08e+01 ... (remaining 44594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9713 17.99 - 35.97: 1300 35.97 - 53.96: 824 53.96 - 71.94: 324 71.94 - 89.93: 138 Dihedral angle restraints: 12299 sinusoidal: 6550 harmonic: 5749 Sorted by residual: dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 200 " pdb=" CB CYS A 200 " ideal model delta sinusoidal sigma weight residual 93.00 179.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " pdb=" SG CYS A 218 " pdb=" CB CYS A 218 " ideal model delta sinusoidal sigma weight residual -86.00 -167.21 81.21 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual -86.00 -5.76 -80.24 1 1.00e+01 1.00e-02 7.97e+01 ... (remaining 12296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1012 0.084 - 0.168: 738 0.168 - 0.252: 239 0.252 - 0.336: 25 0.336 - 0.420: 1 Chirality restraints: 2015 Sorted by residual: chirality pdb=" CA PHE B 695 " pdb=" N PHE B 695 " pdb=" C PHE B 695 " pdb=" CB PHE B 695 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ILE A 34 " pdb=" N ILE A 34 " pdb=" C ILE A 34 " pdb=" CB ILE A 34 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE A 491 " pdb=" CA ILE A 491 " pdb=" CG1 ILE A 491 " pdb=" CG2 ILE A 491 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2012 not shown) Planarity restraints: 3773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 816 " 0.014 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN B 816 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN B 816 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 816 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 816 " -0.765 2.00e-02 2.50e+03 pdb="HD22 ASN B 816 " 0.765 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 168 " 0.020 2.00e-02 2.50e+03 4.42e-01 2.92e+03 pdb=" CG ASN A 168 " 0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN A 168 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 168 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 168 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN A 168 " -0.765 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 520 " 0.027 2.00e-02 2.50e+03 4.42e-01 2.92e+03 pdb=" CG ASN A 520 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 520 " -0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A 520 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 520 " 0.765 2.00e-02 2.50e+03 pdb="HD22 ASN A 520 " -0.763 2.00e-02 2.50e+03 ... (remaining 3770 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.82: 24 1.82 - 2.51: 16852 2.51 - 3.21: 80862 3.21 - 3.90: 106235 3.90 - 4.60: 158835 Nonbonded interactions: 362808 Sorted by model distance: nonbonded pdb=" H LEU B 556 " pdb="HD21 LEU B 556 " model vdw 1.125 2.270 nonbonded pdb=" OE1 GLU A 204 " pdb=" HA GLU A 204 " model vdw 1.423 2.620 nonbonded pdb="HD23 LEU B 866 " pdb=" HZ PHE B 892 " model vdw 1.522 2.270 nonbonded pdb=" HB3 ASP B 586 " pdb=" HB3 ASN B 602 " model vdw 1.570 2.440 nonbonded pdb=" HA LEU A 256 " pdb="HD23 LEU A 256 " model vdw 1.570 2.440 ... (remaining 362803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 193 or (resid 194 and ( \ name N or name CA or name C or name O or name CB or name SG )) or resid 195 thro \ ugh 233 or resid 235 through 298 or (resid 299 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 300 through 384 or resid \ 387 through 574 or resid 576 through 605 or resid 607 through 897)) selection = (chain 'B' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O )) or resid 5 through 119 or resid 123 through 136 or resid 138 through \ 139 or resid 142 through 172 or (resid 173 and (name N or name CA or name C or \ name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or \ name CZ or name OH )) or resid 175 through 197 or resid 199 through 396 or resid \ 398 through 422 or resid 424 through 481 or resid 484 through 488 or (resid 489 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name OD2)) or resid 491 through 498 or resid 500 through 528 or resid 530 throu \ gh 546 or resid 548 through 576 or (resid 577 and (name N or name CA or name C o \ r name O or name CB or name CG or name OD1 or name ND2)) or resid 578 through 61 \ 9 or resid 622 through 897)) } ncs_group { reference = 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 group one per residue 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: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.360 Extract box with map and model: 1.730 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 77.600 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4795 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 : 0.013 0.078 13819 Z= 0.852 Angle : 2.128 10.805 18690 Z= 1.509 Chirality : 0.112 0.420 2015 Planarity : 0.006 0.041 2425 Dihedral : 22.388 88.851 5145 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 5.56 % Allowed : 21.43 % Favored : 73.01 % Rotamer: Outliers : 26.25 % Allowed : 19.00 % Favored : 54.75 % Cbeta Deviations : 0.31 % 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: -5.95 (0.16), residues: 1619 helix: -4.05 (0.21), residues: 193 sheet: -4.35 (0.29), residues: 174 loop : -4.27 (0.14), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP A 176 HIS 0.012 0.003 HIS A 362 PHE 0.041 0.005 PHE A 892 TYR 0.042 0.005 TYR A 496 ARG 0.008 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 326 time to evaluate : 1.790 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6188 (mmt180) REVERT: A 255 ILE cc_start: 0.4429 (OUTLIER) cc_final: 0.4037 (pt) REVERT: A 257 SER cc_start: 0.2673 (OUTLIER) cc_final: 0.1891 (m) REVERT: A 279 SER cc_start: 0.6667 (OUTLIER) cc_final: 0.5845 (t) REVERT: A 333 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6543 (m-40) REVERT: A 455 ARG cc_start: 0.5081 (mmp-170) cc_final: 0.4549 (mtp-110) REVERT: A 493 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.5819 (t80) REVERT: A 556 LEU cc_start: 0.4270 (OUTLIER) cc_final: 0.3579 (mp) REVERT: A 558 MET cc_start: 0.3117 (pmm) cc_final: 0.2419 (ppp) REVERT: A 593 SER cc_start: 0.6451 (OUTLIER) cc_final: 0.5251 (m) REVERT: A 756 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: A 846 GLN cc_start: 0.4525 (OUTLIER) cc_final: 0.4046 (mm110) REVERT: B 144 PRO cc_start: 0.4878 (OUTLIER) cc_final: 0.4590 (Cg_endo) REVERT: B 156 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5517 (ptp) REVERT: B 199 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: B 257 SER cc_start: 0.4251 (OUTLIER) cc_final: 0.3806 (m) REVERT: B 264 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.4582 (pm20) REVERT: B 295 GLU cc_start: 0.6893 (mp0) cc_final: 0.6551 (mp0) REVERT: B 321 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5435 (tm-30) REVERT: B 340 ILE cc_start: 0.5752 (OUTLIER) cc_final: 0.5503 (pt) REVERT: B 378 ILE cc_start: 0.6044 (mm) cc_final: 0.5767 (mm) REVERT: B 391 TYR cc_start: 0.3483 (OUTLIER) cc_final: 0.3227 (t80) REVERT: B 426 VAL cc_start: 0.6131 (OUTLIER) cc_final: 0.5812 (m) REVERT: B 468 THR cc_start: 0.8426 (p) cc_final: 0.8218 (p) REVERT: B 514 CYS cc_start: 0.5348 (OUTLIER) cc_final: 0.5068 (m) REVERT: B 542 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5641 (mmmt) REVERT: B 574 ILE cc_start: 0.5082 (OUTLIER) cc_final: 0.3744 (tt) REVERT: B 580 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.7185 (m) REVERT: B 593 SER cc_start: 0.5375 (OUTLIER) cc_final: 0.4973 (t) REVERT: B 701 PHE cc_start: 0.3350 (OUTLIER) cc_final: 0.2956 (p90) REVERT: C 54 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7075 (mp) REVERT: C 58 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5446 (pt0) REVERT: D 54 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7197 (mp) REVERT: D 58 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6291 (pt0) outliers start: 395 outliers final: 117 residues processed: 617 average time/residue: 0.5324 time to fit residues: 468.5330 Evaluate side-chains 371 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 225 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 374 ASN A 387 ASN A 400 GLN A 451 ASN A 520 ASN A 680 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4852 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 13819 Z= 0.322 Angle : 0.844 9.947 18690 Z= 0.447 Chirality : 0.048 0.252 2015 Planarity : 0.008 0.147 2425 Dihedral : 6.063 29.876 1842 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 33.31 Ramachandran Plot: Outliers : 1.17 % Allowed : 18.59 % Favored : 80.23 % Rotamer: Outliers : 0.53 % Allowed : 4.52 % Favored : 94.95 % 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: -5.78 (0.16), residues: 1619 helix: -3.75 (0.22), residues: 218 sheet: -4.31 (0.27), residues: 205 loop : -4.11 (0.15), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 822 HIS 0.013 0.003 HIS B 30 PHE 0.039 0.003 PHE B 695 TYR 0.027 0.003 TYR B 688 ARG 0.018 0.001 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 265 time to evaluate : 2.100 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: -0.0003 (pptt) cc_final: -0.0561 (pttt) REVERT: A 416 MET cc_start: -0.0516 (mmp) cc_final: -0.0813 (mmp) REVERT: A 521 MET cc_start: 0.4337 (tpt) cc_final: 0.3462 (ttt) REVERT: A 674 LYS cc_start: 0.8972 (mptt) cc_final: 0.8648 (mmmt) REVERT: B 80 LYS cc_start: 0.4351 (mttm) cc_final: 0.3780 (mttt) REVERT: B 213 ASP cc_start: 0.6647 (t0) cc_final: 0.6276 (t0) REVERT: B 354 VAL cc_start: 0.7249 (p) cc_final: 0.6971 (m) REVERT: D 15 GLN cc_start: 0.4824 (tm-30) cc_final: 0.3200 (mm-40) outliers start: 8 outliers final: 2 residues processed: 272 average time/residue: 0.5009 time to fit residues: 198.2670 Evaluate side-chains 208 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 0.0470 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 40.0000 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 397 ASN ** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5101 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 13819 Z= 0.316 Angle : 0.775 8.780 18690 Z= 0.406 Chirality : 0.046 0.231 2015 Planarity : 0.006 0.110 2425 Dihedral : 5.935 34.603 1842 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 1.05 % Allowed : 19.89 % Favored : 79.06 % Rotamer: Outliers : 0.33 % Allowed : 3.52 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.49 (0.17), residues: 1619 helix: -3.60 (0.24), residues: 210 sheet: -4.35 (0.26), residues: 215 loop : -3.82 (0.15), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 402 HIS 0.009 0.002 HIS B 630 PHE 0.059 0.003 PHE A 701 TYR 0.037 0.002 TYR D 60 ARG 0.023 0.001 ARG B 689 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 2.179 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: -0.0084 (pptt) cc_final: -0.0510 (pttt) REVERT: A 375 LEU cc_start: 0.8985 (tp) cc_final: 0.8776 (tt) REVERT: A 416 MET cc_start: -0.0587 (mmp) cc_final: -0.0907 (mmp) REVERT: A 521 MET cc_start: 0.4163 (tpt) cc_final: 0.3844 (ttt) REVERT: B 80 LYS cc_start: 0.4306 (mttm) cc_final: 0.3904 (mttm) REVERT: B 213 ASP cc_start: 0.6790 (t0) cc_final: 0.6411 (t0) REVERT: B 420 PHE cc_start: 0.5593 (m-10) cc_final: 0.5389 (m-10) REVERT: B 471 SER cc_start: 0.8277 (t) cc_final: 0.8048 (m) REVERT: C 58 GLU cc_start: 0.6125 (pp20) cc_final: 0.5428 (pp20) REVERT: D 20 ASP cc_start: 0.8050 (m-30) cc_final: 0.7828 (m-30) outliers start: 5 outliers final: 2 residues processed: 235 average time/residue: 0.5195 time to fit residues: 179.9377 Evaluate side-chains 200 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: