Starting phenix.real_space_refine (version: dev) on Thu Feb 23 01:23:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/02_2023/6zfo_11184_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/02_2023/6zfo_11184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/02_2023/6zfo_11184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/02_2023/6zfo_11184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/02_2023/6zfo_11184_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zfo_11184/02_2023/6zfo_11184_trim.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 Process input model Symmetric amino acids flipped Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18988 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2986 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3272 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "L" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3222 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "A" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2986 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3272 Classifications: {'peptide': 218} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3222 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.78, per 1000 atoms: 0.52 Number of scatterers: 18988 At special positions: 0 Unit cell: (78.02, 137.78, 170.15, 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 38 16.00 O 1900 8.00 N 1612 7.00 C 6128 6.00 H 9310 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 16.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 28 sheets defined 9.4% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.660A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 3.974A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 4.359A pdb=" N ARG E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 404 through 408' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.724A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.680A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.660A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.976A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.361A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.725A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.679A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.017A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.496A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.024A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.864A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 154 through 156 removed outlier: 4.353A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.801A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.017A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.496A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 4 through 7 removed outlier: 6.025A pdb=" N THR C 69 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 10.818A pdb=" N GLN C 27 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N SER C 67 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N ILE C 29 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 11.535A pdb=" N SER C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.944A pdb=" N LEU C 11 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 115 through 119 removed outlier: 5.864A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 154 through 156 removed outlier: 4.354A pdb=" N TRP C 149 " --> pdb=" O GLN C 156 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 948 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: 7.64 Time building geometry restraints manager: 16.64 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: 9310 1.03 - 1.23: 0 1.23 - 1.42: 4328 1.42 - 1.62: 5542 1.62 - 1.81: 44 Bond restraints: 19224 Sorted by residual: bond pdb=" C TYR A 505 " pdb=" N GLN A 506 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.48e-02 4.57e+03 1.73e+00 bond pdb=" C TYR E 505 " pdb=" N GLN E 506 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.48e-02 4.57e+03 1.71e+00 bond pdb=" N ILE A 410 " pdb=" CA ILE A 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.20e+00 bond pdb=" CG LYS C 108 " pdb=" CD LYS C 108 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.11e+00 ... (remaining 19219 not shown) Histogram of bond angle deviations from ideal: 60.29 - 75.03: 2 75.03 - 89.76: 0 89.76 - 104.49: 154 104.49 - 119.23: 25689 119.23 - 133.96: 8694 Bond angle restraints: 34539 Sorted by residual: angle pdb=" C SER B 120 " pdb=" N SER B 121 " pdb=" H SER B 121 " ideal model delta sigma weight residual 123.52 69.02 54.51 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA SER B 121 " pdb=" N SER B 121 " pdb=" H SER B 121 " ideal model delta sigma weight residual 113.22 60.29 52.93 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C SER H 120 " pdb=" N SER H 121 " pdb=" CA SER H 121 " ideal model delta sigma weight residual 123.25 129.32 -6.07 1.69e+00 3.50e-01 1.29e+01 angle pdb=" C SER B 120 " pdb=" N SER B 121 " pdb=" CA SER B 121 " ideal model delta sigma weight residual 123.25 129.31 -6.06 1.69e+00 3.50e-01 1.29e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" C ALA L 51 " ideal model delta sigma weight residual 110.80 116.44 -5.64 2.13e+00 2.20e-01 7.01e+00 ... (remaining 34534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 7445 16.15 - 32.30: 328 32.30 - 48.45: 67 48.45 - 64.60: 22 64.60 - 80.75: 6 Dihedral angle restraints: 7868 sinusoidal: 3494 harmonic: 4374 Sorted by residual: dihedral pdb=" CA TRP B 111 " pdb=" C TRP B 111 " pdb=" N GLY B 112 " pdb=" CA GLY B 112 " ideal model delta harmonic sigma weight residual 180.00 163.74 16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA TRP H 111 " pdb=" C TRP H 111 " pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ASP H 73 " pdb=" CB ASP H 73 " pdb=" CG ASP H 73 " pdb=" OD1 ASP H 73 " ideal model delta sinusoidal sigma weight residual -30.00 -83.26 53.26 1 2.00e+01 2.50e-03 9.64e+00 ... (remaining 7865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 852 0.029 - 0.059: 453 0.059 - 0.088: 60 0.088 - 0.117: 99 0.117 - 0.146: 28 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL E 433 " pdb=" N VAL E 433 " pdb=" C VAL E 433 " pdb=" CB VAL E 433 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1489 not shown) Planarity restraints: 2914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO H 157 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 157 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 402 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C ILE A 402 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE A 402 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG A 403 " -0.007 2.00e-02 2.50e+03 ... (remaining 2911 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 213 2.03 - 2.67: 27339 2.67 - 3.31: 53693 3.31 - 3.96: 72610 3.96 - 4.60: 111007 Nonbonded interactions: 264862 Sorted by model distance: nonbonded pdb=" H SER B 121 " pdb=" HA SER B 121 " model vdw 1.382 1.816 nonbonded pdb="HE22 GLN L 6 " pdb=" O TYR L 86 " model vdw 1.548 1.850 nonbonded pdb="HE22 GLN C 6 " pdb=" O TYR C 86 " model vdw 1.553 1.850 nonbonded pdb="HE21 GLN L 90 " pdb=" OG1 THR L 98 " model vdw 1.619 1.850 nonbonded pdb="HE21 GLN C 90 " pdb=" OG1 THR C 98 " model vdw 1.621 1.850 ... (remaining 264857 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' and (resid 333 through 465 or (resid 466 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH12 or name HH21)) or resid 467 t \ hrough 526 or resid 601)) selection = (chain 'E' and (resid 333 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3 or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) o \ r resid 358 through 395 or (resid 396 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 C \ Z or name OH or name H or name HA or name HB2 or name HB3 or name HD1 or name HD \ 2 or name HE1 or name HE2)) or resid 397 through 526 or resid 601)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 6128 2.51 5 N 1612 2.21 5 O 1900 1.98 5 H 9310 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 10.230 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: 0.300 Extract box with map and model: 36.270 Check model and map are aligned: 0.290 Process input model: 63.090 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5138 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 0.032 9914 Z= 0.182 Angle : 0.552 6.068 13482 Z= 0.316 Chirality : 0.043 0.146 1492 Planarity : 0.003 0.040 1730 Dihedral : 10.399 80.747 3522 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1236 helix: -1.91 (0.57), residues: 68 sheet: -0.18 (0.23), residues: 482 loop : -0.37 (0.24), residues: 686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 241 time to evaluate : 1.672 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: 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 outliers start: 14 outliers final: 4 residues processed: 253 average time/residue: 0.6596 time to fit residues: 219.0009 Evaluate side-chains 162 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.5002 time to fit residues: 4.8548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 9914 Z= 0.303 Angle : 0.640 16.203 13482 Z= 0.351 Chirality : 0.046 0.170 1492 Planarity : 0.005 0.073 1730 Dihedral : 4.874 27.971 1376 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1236 helix: -2.06 (0.54), residues: 68 sheet: -0.23 (0.23), residues: 466 loop : -0.77 (0.23), residues: 702 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 1.719 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 outliers start: 4 outliers final: 2 residues processed: 187 average time/residue: 0.6070 time to fit residues: 148.4883 Evaluate side-chains 151 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2065 time to fit residues: 2.7457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9914 Z= 0.238 Angle : 0.555 15.391 13482 Z= 0.302 Chirality : 0.044 0.157 1492 Planarity : 0.004 0.081 1730 Dihedral : 4.678 22.917 1376 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1236 helix: -1.75 (0.58), residues: 68 sheet: -0.18 (0.23), residues: 466 loop : -0.80 (0.24), residues: 702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.605 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 outliers start: 2 outliers final: 2 residues processed: 176 average time/residue: 0.6386 time to fit residues: 148.0637 Evaluate side-chains 149 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2249 time to fit residues: 2.9249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 9914 Z= 0.389 Angle : 0.706 15.658 13482 Z= 0.388 Chirality : 0.047 0.200 1492 Planarity : 0.005 0.067 1730 Dihedral : 5.453 26.626 1376 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.23), residues: 1236 helix: -1.63 (0.58), residues: 68 sheet: -0.31 (0.23), residues: 466 loop : -1.36 (0.23), residues: 702 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 1.605 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 outliers start: 5 outliers final: 4 residues processed: 168 average time/residue: 0.6349 time to fit residues: 139.3477 Evaluate side-chains 142 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.594 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2089 time to fit residues: 3.7219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 60 optimal weight: 0.0010 chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9914 Z= 0.185 Angle : 0.539 15.449 13482 Z= 0.292 Chirality : 0.044 0.160 1492 Planarity : 0.004 0.062 1730 Dihedral : 4.864 24.068 1376 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1236 helix: -1.33 (0.60), residues: 68 sheet: -0.21 (0.23), residues: 474 loop : -1.19 (0.23), residues: 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.572 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 outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.6042 time to fit residues: 135.2048 Evaluate side-chains 137 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 9914 Z= 0.349 Angle : 0.633 15.671 13482 Z= 0.347 Chirality : 0.046 0.165 1492 Planarity : 0.005 0.060 1730 Dihedral : 5.248 27.289 1376 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1236 helix: -1.37 (0.61), residues: 68 sheet: -0.37 (0.23), residues: 470 loop : -1.46 (0.23), residues: 698 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.467 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 outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.5972 time to fit residues: 124.8140 Evaluate side-chains 127 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 66 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9914 Z= 0.168 Angle : 0.531 15.516 13482 Z= 0.286 Chirality : 0.044 0.169 1492 Planarity : 0.004 0.058 1730 Dihedral : 4.781 24.280 1376 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1236 helix: -1.36 (0.62), residues: 68 sheet: -0.20 (0.23), residues: 470 loop : -1.28 (0.23), residues: 698 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.653 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 outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.6315 time to fit residues: 139.1398 Evaluate side-chains 135 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0170 chunk 70 optimal weight: 0.0980 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9914 Z= 0.181 Angle : 0.524 15.591 13482 Z= 0.282 Chirality : 0.044 0.165 1492 Planarity : 0.004 0.057 1730 Dihedral : 4.632 24.061 1376 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1236 helix: -1.42 (0.63), residues: 68 sheet: -0.18 (0.23), residues: 474 loop : -1.19 (0.23), residues: 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.638 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 outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.6039 time to fit residues: 130.6187 Evaluate side-chains 133 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 115 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9914 Z= 0.186 Angle : 0.518 15.663 13482 Z= 0.278 Chirality : 0.043 0.166 1492 Planarity : 0.004 0.057 1730 Dihedral : 4.580 23.994 1376 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1236 helix: -1.39 (0.63), residues: 68 sheet: -0.06 (0.23), residues: 472 loop : -1.16 (0.24), residues: 696 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.602 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 outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.6180 time to fit residues: 130.6704 Evaluate side-chains 131 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9914 Z= 0.211 Angle : 0.532 15.623 13482 Z= 0.287 Chirality : 0.044 0.166 1492 Planarity : 0.004 0.057 1730 Dihedral : 4.656 25.207 1376 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1236 helix: -1.35 (0.62), residues: 68 sheet: -0.04 (0.23), residues: 474 loop : -1.20 (0.24), residues: 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 396 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.605 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 outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.5879 time to fit residues: 123.7675 Evaluate side-chains 132 residues out of total 1076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 HIS ** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.217585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.192538 restraints weight = 48754.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.195086 restraints weight = 56507.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.192925 restraints weight = 32214.482| |-----------------------------------------------------------------------------| r_work (final): 0.4731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9914 Z= 0.192 Angle : 0.527 15.563 13482 Z= 0.283 Chirality : 0.044 0.167 1492 Planarity : 0.004 0.057 1730 Dihedral : 4.634 24.814 1376 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.24), residues: 1236 helix: -1.32 (0.62), residues: 68 sheet: 0.00 (0.23), residues: 474 loop : -1.17 (0.24), residues: 694 =============================================================================== Job complete usr+sys time: 5122.78 seconds wall clock time: 91 minutes 45.05 seconds (5505.05 seconds total)