Starting phenix.real_space_refine on Thu Feb 15 11:39:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/02_2024/7lig_23375_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/02_2024/7lig_23375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/02_2024/7lig_23375.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/02_2024/7lig_23375.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/02_2024/7lig_23375_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lig_23375/02_2024/7lig_23375_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 8000 2.51 5 N 1940 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ASP 419": "OD1" <-> "OD2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "C PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C ASP 419": "OD1" <-> "OD2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D ASP 419": "OD1" <-> "OD2" Residue "D ARG 422": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12148 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "B" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "C" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "D" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DE3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DE3': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DE3': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DE3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.72, per 1000 atoms: 0.55 Number of scatterers: 12148 At special positions: 0 Unit cell: (114.33, 114.33, 92.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2088 8.00 N 1940 7.00 C 8000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 2.1 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 13 through 30 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.682A pdb=" N CYS A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 104 removed outlier: 4.401A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.726A pdb=" N GLU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 160 removed outlier: 4.339A pdb=" N MET A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 166 No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 198 through 246 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 318 through 365 removed outlier: 4.280A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 407 removed outlier: 3.672A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.719A pdb=" N LEU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 419 through 432 removed outlier: 3.823A pdb=" N GLN A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 Processing helix chain 'B' and resid 13 through 30 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 52 through 74 removed outlier: 3.682A pdb=" N CYS B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 104 removed outlier: 4.401A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.727A pdb=" N GLU B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 160 removed outlier: 4.340A pdb=" N MET B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 198 through 246 Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 318 through 365 removed outlier: 4.278A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 407 removed outlier: 3.672A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.718A pdb=" N LEU B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 416' Processing helix chain 'B' and resid 419 through 432 removed outlier: 3.823A pdb=" N GLN B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 468 Processing helix chain 'C' and resid 13 through 30 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 52 through 74 removed outlier: 3.681A pdb=" N CYS C 74 " --> pdb=" O CYS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 104 removed outlier: 4.401A pdb=" N VAL C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 117 removed outlier: 3.727A pdb=" N GLU C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 160 removed outlier: 4.340A pdb=" N MET C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 198 through 246 Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 318 through 365 removed outlier: 4.279A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 407 removed outlier: 3.672A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 381 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.719A pdb=" N LEU C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 416' Processing helix chain 'C' and resid 419 through 432 removed outlier: 3.823A pdb=" N GLN C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 468 Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 52 through 74 removed outlier: 3.682A pdb=" N CYS D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 104 removed outlier: 4.401A pdb=" N VAL D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 117 removed outlier: 3.727A pdb=" N GLU D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 160 removed outlier: 4.340A pdb=" N MET D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 166 No H-bonds generated for 'chain 'D' and resid 163 through 166' Processing helix chain 'D' and resid 198 through 246 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 318 through 365 removed outlier: 4.279A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 407 removed outlier: 3.671A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 381 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 416 removed outlier: 3.719A pdb=" N LEU D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 416' Processing helix chain 'D' and resid 419 through 432 removed outlier: 3.823A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 468 884 hydrogen bonds defined for protein. 2652 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: 3.47 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1780 1.31 - 1.43: 3527 1.43 - 1.56: 6941 1.56 - 1.68: 4 1.68 - 1.81: 172 Bond restraints: 12424 Sorted by residual: bond pdb=" CAH DE3 D 900 " pdb=" NAM DE3 D 900 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" CAH DE3 C 900 " pdb=" NAM DE3 C 900 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" CAH DE3 B 900 " pdb=" NAM DE3 B 900 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CAH DE3 A 900 " pdb=" NAM DE3 A 900 " ideal model delta sigma weight residual 1.347 1.454 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" CAH DE3 C 900 " pdb=" OAN DE3 C 900 " ideal model delta sigma weight residual 1.226 1.180 0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 12419 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.67: 256 106.67 - 113.52: 7037 113.52 - 120.37: 4988 120.37 - 127.22: 4455 127.22 - 134.07: 116 Bond angle restraints: 16852 Sorted by residual: angle pdb=" N ALA C 215 " pdb=" CA ALA C 215 " pdb=" C ALA C 215 " ideal model delta sigma weight residual 112.17 116.04 -3.87 1.36e+00 5.41e-01 8.09e+00 angle pdb=" N ALA A 215 " pdb=" CA ALA A 215 " pdb=" C ALA A 215 " ideal model delta sigma weight residual 112.17 116.01 -3.84 1.36e+00 5.41e-01 7.99e+00 angle pdb=" N ALA D 215 " pdb=" CA ALA D 215 " pdb=" C ALA D 215 " ideal model delta sigma weight residual 112.17 116.00 -3.83 1.36e+00 5.41e-01 7.94e+00 angle pdb=" N ALA B 215 " pdb=" CA ALA B 215 " pdb=" C ALA B 215 " ideal model delta sigma weight residual 112.17 115.97 -3.80 1.36e+00 5.41e-01 7.81e+00 angle pdb=" C SER B 370 " pdb=" N PHE B 371 " pdb=" CA PHE B 371 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.44e+00 ... (remaining 16847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6404 17.90 - 35.79: 676 35.79 - 53.69: 152 53.69 - 71.58: 32 71.58 - 89.48: 16 Dihedral angle restraints: 7280 sinusoidal: 2772 harmonic: 4508 Sorted by residual: dihedral pdb=" CA ALA A 365 " pdb=" C ALA A 365 " pdb=" N ALA A 366 " pdb=" CA ALA A 366 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA C 365 " pdb=" C ALA C 365 " pdb=" N ALA C 366 " pdb=" CA ALA C 366 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA D 365 " pdb=" C ALA D 365 " pdb=" N ALA D 366 " pdb=" CA ALA D 366 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1125 0.030 - 0.059: 554 0.059 - 0.089: 219 0.089 - 0.118: 80 0.118 - 0.148: 38 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CG LEU C 349 " pdb=" CB LEU C 349 " pdb=" CD1 LEU C 349 " pdb=" CD2 LEU C 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CG LEU D 349 " pdb=" CB LEU D 349 " pdb=" CD1 LEU D 349 " pdb=" CD2 LEU D 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CG LEU B 349 " pdb=" CB LEU B 349 " pdb=" CD1 LEU B 349 " pdb=" CD2 LEU B 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2013 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 195 " 0.053 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO D 196 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 195 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO A 196 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 195 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.90e+00 pdb=" N PRO B 196 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.044 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3999 2.84 - 3.36: 12293 3.36 - 3.87: 19664 3.87 - 4.39: 21547 4.39 - 4.90: 37576 Nonbonded interactions: 95079 Sorted by model distance: nonbonded pdb=" O ILE A 210 " pdb=" OG1 THR A 214 " model vdw 2.328 2.440 nonbonded pdb=" O ILE D 210 " pdb=" OG1 THR D 214 " model vdw 2.328 2.440 nonbonded pdb=" O ILE B 210 " pdb=" OG1 THR B 214 " model vdw 2.329 2.440 nonbonded pdb=" O ILE C 210 " pdb=" OG1 THR C 214 " model vdw 2.329 2.440 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.331 2.440 ... (remaining 95074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.200 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.630 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.006 0.108 12424 Z= 0.369 Angle : 0.801 8.010 16852 Z= 0.468 Chirality : 0.044 0.148 2016 Planarity : 0.008 0.079 2020 Dihedral : 16.002 89.477 4352 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.47 % Allowed : 7.96 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.19), residues: 1500 helix: -0.74 (0.13), residues: 1160 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 20 HIS 0.003 0.001 HIS A 33 PHE 0.023 0.002 PHE A 363 TYR 0.014 0.002 TYR A 380 ARG 0.003 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 248 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.8284 (mtt) cc_final: 0.8051 (mtt) REVERT: C 353 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (m) REVERT: C 377 MET cc_start: 0.8390 (mtt) cc_final: 0.7883 (mtt) REVERT: D 377 MET cc_start: 0.8326 (mtt) cc_final: 0.8062 (mtt) outliers start: 20 outliers final: 4 residues processed: 267 average time/residue: 0.8681 time to fit residues: 258.9428 Evaluate side-chains 153 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 363 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12424 Z= 0.193 Angle : 0.514 6.709 16852 Z= 0.273 Chirality : 0.036 0.125 2016 Planarity : 0.005 0.059 2020 Dihedral : 4.970 55.665 1662 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.17 % Allowed : 18.58 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.22), residues: 1500 helix: 1.24 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 34 HIS 0.006 0.001 HIS A 233 PHE 0.024 0.001 PHE B 183 TYR 0.021 0.002 TYR B 204 ARG 0.007 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 157 time to evaluate : 1.458 Fit side-chains REVERT: A 86 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 377 MET cc_start: 0.8105 (mtt) cc_final: 0.7620 (mtm) REVERT: B 86 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7356 (tt) REVERT: B 377 MET cc_start: 0.8300 (mtt) cc_final: 0.7894 (mtm) REVERT: C 86 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7458 (tt) REVERT: D 86 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7632 (tt) REVERT: D 377 MET cc_start: 0.8277 (mtt) cc_final: 0.7805 (mtm) outliers start: 43 outliers final: 11 residues processed: 184 average time/residue: 0.8564 time to fit residues: 177.5507 Evaluate side-chains 153 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 149 optimal weight: 0.0970 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN C 16 HIS D 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12424 Z= 0.216 Angle : 0.511 6.591 16852 Z= 0.269 Chirality : 0.037 0.126 2016 Planarity : 0.004 0.048 2020 Dihedral : 4.470 38.929 1656 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.88 % Allowed : 21.76 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.22), residues: 1500 helix: 1.80 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.71 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 187 HIS 0.008 0.001 HIS B 46 PHE 0.012 0.001 PHE A 363 TYR 0.017 0.001 TYR C 204 ARG 0.002 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.453 Fit side-chains REVERT: A 86 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7664 (tt) REVERT: A 190 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6436 (m-80) REVERT: A 377 MET cc_start: 0.8030 (mtt) cc_final: 0.7590 (mtm) REVERT: C 86 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7525 (tt) REVERT: D 86 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7656 (tt) outliers start: 39 outliers final: 13 residues processed: 182 average time/residue: 0.9286 time to fit residues: 190.9566 Evaluate side-chains 153 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 146 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 HIS C 469 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12424 Z= 0.215 Angle : 0.520 6.841 16852 Z= 0.269 Chirality : 0.038 0.184 2016 Planarity : 0.003 0.039 2020 Dihedral : 4.410 39.388 1656 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.95 % Allowed : 23.38 % Favored : 73.67 % 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: 2.32 (0.22), residues: 1500 helix: 2.09 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 34 HIS 0.007 0.001 HIS B 233 PHE 0.008 0.001 PHE C 450 TYR 0.015 0.001 TYR B 204 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 86 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 190 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: A 377 MET cc_start: 0.8028 (mtt) cc_final: 0.7664 (mtm) REVERT: C 239 MET cc_start: 0.7804 (ttm) cc_final: 0.7516 (mtm) REVERT: D 239 MET cc_start: 0.7748 (ttm) cc_final: 0.7505 (mtm) outliers start: 40 outliers final: 19 residues processed: 170 average time/residue: 0.8083 time to fit residues: 155.6680 Evaluate side-chains 158 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12424 Z= 0.195 Angle : 0.510 7.191 16852 Z= 0.263 Chirality : 0.037 0.164 2016 Planarity : 0.003 0.034 2020 Dihedral : 4.341 39.450 1656 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.51 % Allowed : 23.89 % Favored : 73.60 % 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: 2.46 (0.23), residues: 1500 helix: 2.17 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 20 HIS 0.007 0.001 HIS B 233 PHE 0.014 0.001 PHE B 223 TYR 0.025 0.001 TYR B 128 ARG 0.002 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.347 Fit side-chains REVERT: A 190 PHE cc_start: 0.6673 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: A 377 MET cc_start: 0.7967 (mtt) cc_final: 0.7636 (mtm) REVERT: D 377 MET cc_start: 0.7840 (mtm) cc_final: 0.7553 (mtm) outliers start: 34 outliers final: 16 residues processed: 167 average time/residue: 0.8068 time to fit residues: 152.7251 Evaluate side-chains 152 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 469 ASN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12424 Z= 0.192 Angle : 0.517 9.131 16852 Z= 0.264 Chirality : 0.037 0.162 2016 Planarity : 0.003 0.031 2020 Dihedral : 4.333 38.797 1656 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.73 % Allowed : 23.53 % Favored : 73.75 % 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: 2.59 (0.23), residues: 1500 helix: 2.23 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.28 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 20 HIS 0.006 0.001 HIS A 233 PHE 0.012 0.001 PHE A 363 TYR 0.028 0.001 TYR C 128 ARG 0.001 0.000 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.7915 (mtt) cc_final: 0.7583 (mtm) outliers start: 37 outliers final: 18 residues processed: 174 average time/residue: 0.7992 time to fit residues: 157.1248 Evaluate side-chains 155 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.0170 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12424 Z= 0.189 Angle : 0.532 9.923 16852 Z= 0.270 Chirality : 0.037 0.162 2016 Planarity : 0.003 0.030 2020 Dihedral : 4.331 38.639 1656 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.99 % Allowed : 24.78 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.23), residues: 1500 helix: 2.25 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.22 (0.41), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 20 HIS 0.007 0.001 HIS B 233 PHE 0.020 0.001 PHE A 363 TYR 0.025 0.001 TYR C 128 ARG 0.002 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.7838 (mtt) cc_final: 0.7523 (mtm) REVERT: B 190 PHE cc_start: 0.6859 (m-80) cc_final: 0.6597 (m-80) REVERT: C 190 PHE cc_start: 0.6738 (m-80) cc_final: 0.6439 (m-80) REVERT: D 407 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7651 (t-90) outliers start: 27 outliers final: 16 residues processed: 171 average time/residue: 0.8125 time to fit residues: 157.3910 Evaluate side-chains 155 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 317 ASP Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 407 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN D 84 ASN D 469 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12424 Z= 0.163 Angle : 0.518 9.788 16852 Z= 0.267 Chirality : 0.036 0.163 2016 Planarity : 0.003 0.029 2020 Dihedral : 4.315 38.317 1656 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.11 % Allowed : 25.88 % Favored : 73.01 % 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: 2.78 (0.23), residues: 1500 helix: 2.37 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 155 HIS 0.006 0.001 HIS B 233 PHE 0.011 0.001 PHE D 363 TYR 0.029 0.001 TYR C 128 ARG 0.002 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.7650 (mtt) cc_final: 0.7391 (mtm) REVERT: B 454 MET cc_start: 0.6576 (ttt) cc_final: 0.6343 (ttt) REVERT: C 190 PHE cc_start: 0.6652 (m-80) cc_final: 0.6342 (m-80) REVERT: D 377 MET cc_start: 0.7840 (mtm) cc_final: 0.7482 (mtm) outliers start: 15 outliers final: 13 residues processed: 170 average time/residue: 0.8120 time to fit residues: 156.1431 Evaluate side-chains 157 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 317 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12424 Z= 0.187 Angle : 0.554 9.402 16852 Z= 0.282 Chirality : 0.037 0.168 2016 Planarity : 0.003 0.028 2020 Dihedral : 4.325 39.509 1656 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.33 % Allowed : 26.18 % Favored : 72.49 % 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: 2.76 (0.23), residues: 1500 helix: 2.36 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 155 HIS 0.005 0.001 HIS B 233 PHE 0.024 0.001 PHE D 363 TYR 0.040 0.002 TYR C 128 ARG 0.002 0.000 ARG C 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.356 Fit side-chains REVERT: A 377 MET cc_start: 0.7688 (mtt) cc_final: 0.7424 (mtm) REVERT: A 458 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6346 (mpp) REVERT: B 190 PHE cc_start: 0.6714 (m-80) cc_final: 0.6393 (m-80) REVERT: B 377 MET cc_start: 0.7703 (mtm) cc_final: 0.7305 (mtm) REVERT: C 190 PHE cc_start: 0.6658 (m-80) cc_final: 0.6288 (m-80) outliers start: 18 outliers final: 8 residues processed: 168 average time/residue: 0.8837 time to fit residues: 167.2058 Evaluate side-chains 155 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 317 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12424 Z= 0.190 Angle : 0.549 9.087 16852 Z= 0.283 Chirality : 0.038 0.177 2016 Planarity : 0.003 0.028 2020 Dihedral : 4.370 39.600 1656 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.74 % Allowed : 27.58 % Favored : 71.68 % 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: 2.77 (0.23), residues: 1500 helix: 2.36 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.21 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 155 HIS 0.014 0.001 HIS B 233 PHE 0.010 0.001 PHE B 223 TYR 0.038 0.002 TYR A 128 ARG 0.002 0.000 ARG D 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.339 Fit side-chains REVERT: A 377 MET cc_start: 0.7637 (mtt) cc_final: 0.7380 (mtm) REVERT: A 454 MET cc_start: 0.7266 (tmm) cc_final: 0.6917 (ttt) REVERT: B 190 PHE cc_start: 0.6728 (m-80) cc_final: 0.6383 (m-80) REVERT: B 377 MET cc_start: 0.7593 (mtm) cc_final: 0.7187 (mtm) outliers start: 10 outliers final: 12 residues processed: 166 average time/residue: 0.8659 time to fit residues: 161.6488 Evaluate side-chains 156 residues out of total 1356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 233 HIS Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 317 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 0.0010 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 0.0170 chunk 6 optimal weight: 0.0980 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.101644 restraints weight = 20161.585| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.47 r_work: 0.3292 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12424 Z= 0.172 Angle : 0.550 8.996 16852 Z= 0.283 Chirality : 0.038 0.174 2016 Planarity : 0.003 0.028 2020 Dihedral : 4.370 38.382 1656 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.74 % Allowed : 28.17 % Favored : 71.09 % 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: 2.81 (0.23), residues: 1500 helix: 2.38 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.15 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 155 HIS 0.011 0.001 HIS B 233 PHE 0.017 0.001 PHE C 363 TYR 0.037 0.002 TYR C 128 ARG 0.002 0.000 ARG D 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3570.56 seconds wall clock time: 65 minutes 11.77 seconds (3911.77 seconds total)