Starting phenix.real_space_refine on Thu Feb 15 13:37:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkq_14765/02_2024/7zkq_14765_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkq_14765/02_2024/7zkq_14765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkq_14765/02_2024/7zkq_14765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkq_14765/02_2024/7zkq_14765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkq_14765/02_2024/7zkq_14765_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkq_14765/02_2024/7zkq_14765_updated.pdb" } resolution = 3.15 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= 0.102 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 52 5.16 5 C 8063 2.51 5 N 1987 2.21 5 O 2245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 622": "OD1" <-> "OD2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C TYR 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 791": "OE1" <-> "OE2" Residue "C GLU 797": "OE1" <-> "OE2" Residue "C ASP 825": "OD1" <-> "OD2" Residue "T GLU 58": "OE1" <-> "OE2" Residue "T GLU 66": "OE1" <-> "OE2" Residue "T PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 12352 Number of models: 1 Model: "" Number of chains: 8 Chain: "2" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3609 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 502 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1752 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 15, 'TRANS': 201} Chain breaks: 1 Chain: "C" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3396 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 13, 'TRANS': 402} Chain: "T" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2844 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'CDL:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'CDL': 1, 'PLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.16, per 1000 atoms: 0.58 Number of scatterers: 12352 At special positions: 0 Unit cell: (112.271, 140.036, 132.793, 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 52 16.00 P 5 15.00 O 2245 8.00 N 1987 7.00 C 8063 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: 4.85 Conformation dependent library (CDL) restraints added in 2.1 seconds 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 6 sheets defined 56.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain '2' and resid 3 through 14 Processing helix chain '2' and resid 23 through 46 Processing helix chain '2' and resid 63 through 84 Processing helix chain '2' and resid 91 through 96 Processing helix chain '2' and resid 101 through 118 Processing helix chain '2' and resid 123 through 143 Processing helix chain '2' and resid 148 through 174 Processing helix chain '2' and resid 198 through 212 removed outlier: 3.920A pdb=" N LYS 2 211 " --> pdb=" O GLY 2 207 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 217 No H-bonds generated for 'chain '2' and resid 215 through 217' Processing helix chain '2' and resid 219 through 226 Processing helix chain '2' and resid 230 through 236 removed outlier: 4.673A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 239 through 250 Processing helix chain '2' and resid 258 through 277 removed outlier: 4.046A pdb=" N LEU 2 277 " --> pdb=" O VAL 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 301 removed outlier: 3.931A pdb=" N LEU 2 299 " --> pdb=" O TYR 2 295 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU 2 300 " --> pdb=" O MET 2 296 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU 2 301 " --> pdb=" O MET 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 333 removed outlier: 3.501A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR 2 333 " --> pdb=" O PHE 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 350 Processing helix chain '2' and resid 353 through 355 No H-bonds generated for 'chain '2' and resid 353 through 355' Processing helix chain '2' and resid 358 through 372 Processing helix chain '2' and resid 378 through 391 Processing helix chain '2' and resid 397 through 420 removed outlier: 3.683A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 466 removed outlier: 5.660A pdb=" N PHE 2 454 " --> pdb=" O ILE 2 450 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE 2 455 " --> pdb=" O THR 2 451 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR 2 456 " --> pdb=" O PHE 2 452 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 2 457 " --> pdb=" O GLY 2 453 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER 2 458 " --> pdb=" O PHE 2 454 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU 2 459 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 24 Processing helix chain 'b' and resid 33 through 66 removed outlier: 3.649A pdb=" N VAL b 37 " --> pdb=" O PRO b 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 27 through 29 No H-bonds generated for 'chain 'A' and resid 27 through 29' Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'C' and resid 431 through 444 Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 468 through 482 removed outlier: 3.848A pdb=" N GLU C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 504 through 506 No H-bonds generated for 'chain 'C' and resid 504 through 506' Processing helix chain 'C' and resid 510 through 522 removed outlier: 3.712A pdb=" N ALA C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 537 removed outlier: 3.655A pdb=" N GLN C 537 " --> pdb=" O PHE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 566 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 590 through 602 removed outlier: 3.648A pdb=" N TYR C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 622 Processing helix chain 'C' and resid 631 through 644 Processing helix chain 'C' and resid 647 through 659 removed outlier: 3.670A pdb=" N LEU C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 679 Processing helix chain 'C' and resid 683 through 694 Processing helix chain 'C' and resid 704 through 713 Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 729 through 731 No H-bonds generated for 'chain 'C' and resid 729 through 731' Processing helix chain 'C' and resid 737 through 750 removed outlier: 3.537A pdb=" N THR C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 767 removed outlier: 4.745A pdb=" N GLU C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 782 Processing helix chain 'C' and resid 786 through 799 Processing helix chain 'C' and resid 801 through 809 Processing helix chain 'C' and resid 827 through 843 removed outlier: 3.738A pdb=" N ALA C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 17 Processing helix chain 'T' and resid 22 through 45 Processing helix chain 'T' and resid 53 through 66 Processing helix chain 'T' and resid 81 through 87 removed outlier: 3.532A pdb=" N VAL T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP T 86 " --> pdb=" O ASP T 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY T 87 " --> pdb=" O PRO T 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 81 through 87' Processing helix chain 'T' and resid 91 through 95 removed outlier: 4.525A pdb=" N TRP T 95 " --> pdb=" O ASP T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 99 No H-bonds generated for 'chain 'T' and resid 97 through 99' Processing helix chain 'T' and resid 121 through 123 No H-bonds generated for 'chain 'T' and resid 121 through 123' Processing helix chain 'T' and resid 139 through 148 Processing helix chain 'T' and resid 205 through 212 Processing helix chain 'T' and resid 228 through 230 No H-bonds generated for 'chain 'T' and resid 228 through 230' Processing helix chain 'T' and resid 262 through 278 Processing helix chain 'T' and resid 290 through 293 No H-bonds generated for 'chain 'T' and resid 290 through 293' Processing helix chain 'T' and resid 296 through 319 removed outlier: 3.647A pdb=" N LEU T 318 " --> pdb=" O GLU T 314 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR T 319 " --> pdb=" O LYS T 315 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 331 removed outlier: 3.833A pdb=" N LYS T 331 " --> pdb=" O PRO T 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 328 through 331' Processing helix chain 'T' and resid 333 through 336 Processing helix chain 'T' and resid 349 through 351 No H-bonds generated for 'chain 'T' and resid 349 through 351' Processing sheet with id= A, first strand: chain '2' and resid 52 through 54 removed outlier: 3.885A pdb=" N LEU 2 59 " --> pdb=" O VAL 2 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 removed outlier: 5.491A pdb=" N VAL A 176 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 117 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 43 through 49 removed outlier: 3.691A pdb=" N THR A 43 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 63 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG A 109 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A 195 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A 107 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A 197 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS A 105 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.654A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'T' and resid 48 through 51 removed outlier: 6.767A pdb=" N ILE T 252 " --> pdb=" O ASP T 49 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LYS T 51 " --> pdb=" O ILE T 252 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE T 254 " --> pdb=" O LYS T 51 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'T' and resid 180 through 184 removed outlier: 6.538A pdb=" N LEU T 70 " --> pdb=" O VAL T 181 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N PHE T 183 " --> pdb=" O LEU T 70 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR T 72 " --> pdb=" O PHE T 183 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE T 219 " --> pdb=" O LEU T 71 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL T 73 " --> pdb=" O ILE T 219 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL T 221 " --> pdb=" O VAL T 73 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 612 hydrogen bonds defined for protein. 1800 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: 3.28 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1936 1.31 - 1.44: 3418 1.44 - 1.56: 7167 1.56 - 1.68: 24 1.68 - 1.81: 93 Bond restraints: 12638 Sorted by residual: bond pdb=" C1 LMN C 901 " pdb=" O5 LMN C 901 " ideal model delta sigma weight residual 1.403 1.494 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CBS LMN C 901 " pdb=" CCM LMN C 901 " ideal model delta sigma weight residual 1.529 1.620 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" CBJ LMN C 901 " pdb=" CBL LMN C 901 " ideal model delta sigma weight residual 1.525 1.612 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C5 LMN C 901 " pdb=" O5 LMN C 901 " ideal model delta sigma weight residual 1.413 1.495 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CCF LMN C 901 " pdb=" OBX LMN C 901 " ideal model delta sigma weight residual 1.410 1.491 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 12633 not shown) Histogram of bond angle deviations from ideal: 96.26 - 103.82: 166 103.82 - 111.38: 5495 111.38 - 118.95: 4706 118.95 - 126.51: 6582 126.51 - 134.08: 173 Bond angle restraints: 17122 Sorted by residual: angle pdb=" N ILE 2 232 " pdb=" CA ILE 2 232 " pdb=" C ILE 2 232 " ideal model delta sigma weight residual 111.81 107.90 3.91 8.60e-01 1.35e+00 2.07e+01 angle pdb=" CA PHE A 154 " pdb=" C PHE A 154 " pdb=" O PHE A 154 " ideal model delta sigma weight residual 121.47 116.74 4.73 1.15e+00 7.56e-01 1.69e+01 angle pdb=" C GLY T 105 " pdb=" N ALA T 106 " pdb=" CA ALA T 106 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C ALA A 3 " pdb=" N ASN A 4 " pdb=" CA ASN A 4 " ideal model delta sigma weight residual 120.09 124.85 -4.76 1.25e+00 6.40e-01 1.45e+01 angle pdb=" N ILE A 151 " pdb=" CA ILE A 151 " pdb=" C ILE A 151 " ideal model delta sigma weight residual 112.50 107.39 5.11 1.39e+00 5.18e-01 1.35e+01 ... (remaining 17117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 7383 34.11 - 68.22: 207 68.22 - 102.34: 38 102.34 - 136.45: 18 136.45 - 170.56: 2 Dihedral angle restraints: 7648 sinusoidal: 3238 harmonic: 4410 Sorted by residual: dihedral pdb=" C3 PLC T 401 " pdb=" C1 PLC T 401 " pdb=" C2 PLC T 401 " pdb=" O3P PLC T 401 " ideal model delta sinusoidal sigma weight residual 67.16 -122.28 -170.56 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC T 401 " pdb=" C1 PLC T 401 " pdb=" C2 PLC T 401 " pdb=" O3P PLC T 401 " ideal model delta sinusoidal sigma weight residual -55.71 112.91 -168.62 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C1B PLC T 401 " pdb=" CB PLC T 401 " pdb=" O3 PLC T 401 " pdb=" C3 PLC T 401 " ideal model delta sinusoidal sigma weight residual -178.77 -42.42 -136.35 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 7645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1431 0.043 - 0.085: 381 0.085 - 0.127: 102 0.127 - 0.170: 10 0.170 - 0.212: 4 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA ILE A 155 " pdb=" N ILE A 155 " pdb=" C ILE A 155 " pdb=" CB ILE A 155 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CCV LMN C 901 " pdb=" CCR LMN C 901 " pdb=" CCT LMN C 901 " pdb=" OAU LMN C 901 " both_signs ideal model delta sigma weight residual False 2.28 2.47 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 1925 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU T 332 " -0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO T 333 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO T 333 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO T 333 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 530 " 0.013 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE C 530 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 530 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 530 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 530 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 530 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 530 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR 2 228 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO 2 229 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO 2 229 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO 2 229 " -0.025 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 218 2.68 - 3.24: 12156 3.24 - 3.79: 19836 3.79 - 4.35: 26678 4.35 - 4.90: 43736 Nonbonded interactions: 102624 Sorted by model distance: nonbonded pdb=" OH TYR C 782 " pdb=" OD1 ASP C 839 " model vdw 2.128 2.440 nonbonded pdb=" OH TYR 2 67 " pdb=" OG1 THR 2 314 " model vdw 2.148 2.440 nonbonded pdb=" OD2 ASP 2 39 " pdb=" OH TYR 2 73 " model vdw 2.221 2.440 nonbonded pdb=" O ILE 2 224 " pdb=" OG1 THR 2 228 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP C 573 " pdb=" NH1 ARG C 606 " model vdw 2.261 2.520 ... (remaining 102619 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.580 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 34.960 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 0.005 0.091 12638 Z= 0.347 Angle : 0.646 9.904 17122 Z= 0.343 Chirality : 0.042 0.212 1928 Planarity : 0.004 0.103 2118 Dihedral : 17.818 170.559 4814 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 0.23 % Allowed : 0.30 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.28 (0.22), residues: 1481 helix: 1.89 (0.18), residues: 844 sheet: -0.56 (0.52), residues: 91 loop : -0.53 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.032 0.001 PHE C 530 TYR 0.014 0.001 TYR A 194 ARG 0.007 0.000 ARG T 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7231 (tpt) cc_final: 0.6906 (tpt) REVERT: 2 395 TYR cc_start: 0.8272 (m-10) cc_final: 0.7956 (m-10) REVERT: C 793 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7418 (tt0) REVERT: C 798 LYS cc_start: 0.7700 (tttm) cc_final: 0.7492 (mptt) REVERT: C 805 LEU cc_start: 0.8222 (tt) cc_final: 0.7801 (mp) REVERT: C 811 ASP cc_start: 0.7662 (m-30) cc_final: 0.7315 (t0) outliers start: 3 outliers final: 2 residues processed: 207 average time/residue: 0.2584 time to fit residues: 76.4487 Evaluate side-chains 143 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 392 ASN b 22 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 833 GLN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12638 Z= 0.179 Angle : 0.540 8.824 17122 Z= 0.265 Chirality : 0.039 0.180 1928 Planarity : 0.003 0.063 2118 Dihedral : 14.374 167.622 1928 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer: Outliers : 0.98 % Allowed : 5.12 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.48 (0.22), residues: 1481 helix: 2.10 (0.18), residues: 846 sheet: -0.50 (0.53), residues: 93 loop : -0.54 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 102 HIS 0.005 0.001 HIS C 583 PHE 0.027 0.001 PHE C 530 TYR 0.018 0.001 TYR 2 412 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7155 (tpt) cc_final: 0.6811 (tpt) REVERT: 2 395 TYR cc_start: 0.8213 (m-10) cc_final: 0.8007 (m-10) REVERT: A 66 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7613 (mt) REVERT: A 82 MET cc_start: 0.7554 (ppp) cc_final: 0.7015 (ptp) REVERT: A 152 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: C 805 LEU cc_start: 0.8167 (tt) cc_final: 0.7699 (mp) REVERT: C 811 ASP cc_start: 0.7629 (m-30) cc_final: 0.7340 (t0) REVERT: T 315 LYS cc_start: 0.7404 (ttpt) cc_final: 0.7144 (ttpt) outliers start: 13 outliers final: 8 residues processed: 162 average time/residue: 0.2430 time to fit residues: 56.4819 Evaluate side-chains 141 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain T residue 88 MET Chi-restraints excluded: chain T residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.0970 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 119 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 392 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12638 Z= 0.219 Angle : 0.521 8.324 17122 Z= 0.261 Chirality : 0.039 0.189 1928 Planarity : 0.003 0.052 2118 Dihedral : 12.351 169.048 1926 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 1.36 % Allowed : 6.86 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.42 (0.22), residues: 1481 helix: 2.05 (0.18), residues: 848 sheet: -0.33 (0.50), residues: 99 loop : -0.60 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 30 HIS 0.004 0.001 HIS 2 320 PHE 0.025 0.001 PHE C 530 TYR 0.017 0.001 TYR 2 412 ARG 0.009 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7169 (tpt) cc_final: 0.6840 (tpt) REVERT: 2 222 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6573 (mt) REVERT: 2 395 TYR cc_start: 0.8278 (m-10) cc_final: 0.8003 (m-10) REVERT: A 66 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7697 (mt) REVERT: A 74 MET cc_start: 0.6484 (mmp) cc_final: 0.5669 (ttp) REVERT: A 82 MET cc_start: 0.7558 (ppp) cc_final: 0.7116 (ptp) REVERT: A 152 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.6550 (m-30) REVERT: C 682 ASP cc_start: 0.7814 (t0) cc_final: 0.7336 (t70) REVERT: C 805 LEU cc_start: 0.8167 (tt) cc_final: 0.7755 (mp) REVERT: C 811 ASP cc_start: 0.7727 (m-30) cc_final: 0.7419 (t0) REVERT: C 842 MET cc_start: 0.7110 (mtp) cc_final: 0.6732 (mtp) outliers start: 18 outliers final: 10 residues processed: 156 average time/residue: 0.2314 time to fit residues: 54.0271 Evaluate side-chains 149 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain T residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12638 Z= 0.230 Angle : 0.516 13.827 17122 Z= 0.260 Chirality : 0.039 0.158 1928 Planarity : 0.003 0.047 2118 Dihedral : 11.830 169.127 1926 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 1.36 % Allowed : 8.59 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.30 (0.22), residues: 1481 helix: 1.95 (0.18), residues: 853 sheet: -0.67 (0.50), residues: 100 loop : -0.62 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.022 0.001 PHE C 530 TYR 0.015 0.001 TYR 2 157 ARG 0.006 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7211 (tpt) cc_final: 0.6873 (tpt) REVERT: 2 222 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6730 (mt) REVERT: 2 395 TYR cc_start: 0.8329 (m-10) cc_final: 0.8051 (m-10) REVERT: A 66 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 82 MET cc_start: 0.7644 (ppp) cc_final: 0.7194 (ptp) REVERT: A 152 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.6507 (m-30) REVERT: A 174 TYR cc_start: 0.8491 (m-80) cc_final: 0.8262 (m-10) REVERT: A 183 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7500 (ttp-170) REVERT: C 606 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.6438 (mmm-85) REVERT: C 805 LEU cc_start: 0.8221 (tt) cc_final: 0.7856 (mp) REVERT: C 811 ASP cc_start: 0.7817 (m-30) cc_final: 0.7528 (t0) REVERT: C 842 MET cc_start: 0.7226 (mtp) cc_final: 0.6767 (mtp) outliers start: 18 outliers final: 12 residues processed: 150 average time/residue: 0.2381 time to fit residues: 53.3055 Evaluate side-chains 150 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 50.0000 chunk 127 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 227 ASN ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12638 Z= 0.186 Angle : 0.493 12.722 17122 Z= 0.249 Chirality : 0.038 0.136 1928 Planarity : 0.003 0.048 2118 Dihedral : 11.610 170.045 1926 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Rotamer: Outliers : 1.73 % Allowed : 9.34 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.41 (0.22), residues: 1481 helix: 2.03 (0.18), residues: 854 sheet: -0.50 (0.50), residues: 103 loop : -0.60 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 795 HIS 0.004 0.001 HIS 2 320 PHE 0.025 0.001 PHE 2 46 TYR 0.016 0.001 TYR 2 412 ARG 0.005 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7199 (tpt) cc_final: 0.6859 (tpt) REVERT: 2 222 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6833 (mt) REVERT: 2 395 TYR cc_start: 0.8323 (m-10) cc_final: 0.8071 (m-10) REVERT: A 66 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 82 MET cc_start: 0.7594 (ppp) cc_final: 0.7149 (ptp) REVERT: A 152 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6503 (m-30) REVERT: A 183 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7478 (ttp-170) REVERT: C 682 ASP cc_start: 0.8184 (t0) cc_final: 0.7848 (t0) REVERT: C 793 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7601 (tt0) REVERT: C 805 LEU cc_start: 0.8209 (tt) cc_final: 0.7854 (mp) REVERT: C 811 ASP cc_start: 0.7833 (m-30) cc_final: 0.7538 (t0) REVERT: C 842 MET cc_start: 0.7228 (mtp) cc_final: 0.6750 (mtp) outliers start: 23 outliers final: 16 residues processed: 157 average time/residue: 0.2320 time to fit residues: 55.1740 Evaluate side-chains 156 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 70 MET Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.0770 chunk 127 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 50.0000 chunk 137 optimal weight: 0.0870 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12638 Z= 0.153 Angle : 0.477 13.050 17122 Z= 0.240 Chirality : 0.038 0.131 1928 Planarity : 0.003 0.067 2118 Dihedral : 11.387 170.997 1926 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 1.73 % Allowed : 10.40 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.53 (0.22), residues: 1481 helix: 2.13 (0.18), residues: 855 sheet: -0.66 (0.49), residues: 107 loop : -0.51 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 795 HIS 0.004 0.001 HIS 2 320 PHE 0.016 0.001 PHE C 530 TYR 0.017 0.001 TYR 2 412 ARG 0.006 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7181 (tpt) cc_final: 0.6833 (tpt) REVERT: 2 222 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6788 (mt) REVERT: 2 391 LEU cc_start: 0.8095 (mt) cc_final: 0.7860 (mt) REVERT: 2 395 TYR cc_start: 0.8311 (m-10) cc_final: 0.8062 (m-10) REVERT: A 82 MET cc_start: 0.7597 (ppp) cc_final: 0.7143 (ptp) REVERT: C 793 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7291 (tt0) REVERT: C 805 LEU cc_start: 0.8189 (tt) cc_final: 0.7868 (mp) REVERT: C 842 MET cc_start: 0.7286 (mtp) cc_final: 0.6801 (mtp) outliers start: 23 outliers final: 16 residues processed: 141 average time/residue: 0.2294 time to fit residues: 48.5555 Evaluate side-chains 147 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 79 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 86 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN C 607 GLN T 151 ASN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12638 Z= 0.339 Angle : 0.579 15.275 17122 Z= 0.290 Chirality : 0.041 0.152 1928 Planarity : 0.004 0.064 2118 Dihedral : 11.600 166.926 1924 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 1.73 % Allowed : 11.38 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.07 (0.22), residues: 1481 helix: 1.74 (0.18), residues: 853 sheet: -0.79 (0.51), residues: 100 loop : -0.67 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 102 HIS 0.006 0.001 HIS 2 320 PHE 0.024 0.002 PHE C 599 TYR 0.017 0.002 TYR 2 67 ARG 0.006 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 155 MET cc_start: 0.7302 (tpt) cc_final: 0.6947 (tpt) REVERT: 2 222 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6859 (mt) REVERT: 2 395 TYR cc_start: 0.8384 (m-10) cc_final: 0.8142 (m-10) REVERT: A 82 MET cc_start: 0.7648 (ppp) cc_final: 0.7208 (ptp) REVERT: C 793 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7280 (tt0) REVERT: C 805 LEU cc_start: 0.8227 (tt) cc_final: 0.7895 (mp) REVERT: C 842 MET cc_start: 0.7318 (mtp) cc_final: 0.6832 (mtp) REVERT: T 357 ARG cc_start: 0.7649 (mtp85) cc_final: 0.6882 (mmp80) outliers start: 23 outliers final: 17 residues processed: 147 average time/residue: 0.2263 time to fit residues: 49.8357 Evaluate side-chains 147 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 54 HIS ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 794 GLN T 152 ASN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12638 Z= 0.224 Angle : 0.517 13.913 17122 Z= 0.261 Chirality : 0.039 0.138 1928 Planarity : 0.004 0.058 2118 Dihedral : 11.428 167.301 1924 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Rotamer: Outliers : 2.03 % Allowed : 11.08 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.15 (0.22), residues: 1481 helix: 1.82 (0.18), residues: 855 sheet: -0.77 (0.51), residues: 100 loop : -0.65 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.024 0.001 PHE C 599 TYR 0.016 0.001 TYR 2 412 ARG 0.007 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7315 (OUTLIER) cc_final: 0.6537 (t80) REVERT: 2 155 MET cc_start: 0.7271 (tpt) cc_final: 0.6936 (tpt) REVERT: 2 222 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6916 (mt) REVERT: 2 395 TYR cc_start: 0.8384 (m-10) cc_final: 0.8164 (m-10) REVERT: A 82 MET cc_start: 0.7655 (ppp) cc_final: 0.7205 (ptp) REVERT: C 599 PHE cc_start: 0.8053 (t80) cc_final: 0.7794 (t80) REVERT: C 793 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7264 (tt0) REVERT: C 805 LEU cc_start: 0.8210 (tt) cc_final: 0.7894 (mp) REVERT: C 842 MET cc_start: 0.7284 (mtp) cc_final: 0.6757 (mtp) REVERT: T 141 MET cc_start: 0.6324 (mmt) cc_final: 0.6110 (mmt) REVERT: T 357 ARG cc_start: 0.7560 (mtp85) cc_final: 0.6861 (mmp80) outliers start: 27 outliers final: 17 residues processed: 150 average time/residue: 0.2238 time to fit residues: 51.2283 Evaluate side-chains 149 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 70 MET Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 794 GLN ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12638 Z= 0.191 Angle : 0.507 16.418 17122 Z= 0.253 Chirality : 0.038 0.142 1928 Planarity : 0.003 0.056 2118 Dihedral : 11.262 168.114 1924 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 11.45 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.28 (0.22), residues: 1481 helix: 1.94 (0.18), residues: 856 sheet: -0.91 (0.48), residues: 111 loop : -0.58 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.023 0.001 PHE C 599 TYR 0.017 0.001 TYR 2 412 ARG 0.008 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6839 (t80) REVERT: 2 155 MET cc_start: 0.7244 (tpt) cc_final: 0.6908 (tpt) REVERT: 2 222 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6880 (mt) REVERT: 2 395 TYR cc_start: 0.8348 (m-10) cc_final: 0.8125 (m-10) REVERT: A 50 ARG cc_start: 0.7583 (ttm110) cc_final: 0.7174 (mtt90) REVERT: A 82 MET cc_start: 0.7629 (ppp) cc_final: 0.7161 (ptp) REVERT: C 793 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7252 (tt0) REVERT: C 805 LEU cc_start: 0.8202 (tt) cc_final: 0.7888 (mp) REVERT: C 842 MET cc_start: 0.7273 (mtp) cc_final: 0.6756 (mtp) REVERT: T 141 MET cc_start: 0.6373 (mmt) cc_final: 0.6102 (mmt) REVERT: T 247 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7914 (p0) REVERT: T 357 ARG cc_start: 0.7534 (mtp85) cc_final: 0.6802 (mmp80) outliers start: 22 outliers final: 17 residues processed: 136 average time/residue: 0.2376 time to fit residues: 50.3547 Evaluate side-chains 140 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 247 ASN Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 342 VAL Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 152 ASN ** T 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12638 Z= 0.199 Angle : 0.512 16.359 17122 Z= 0.255 Chirality : 0.038 0.135 1928 Planarity : 0.003 0.048 2118 Dihedral : 11.202 167.871 1924 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Rotamer: Outliers : 1.81 % Allowed : 11.15 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.31 (0.22), residues: 1481 helix: 1.98 (0.18), residues: 855 sheet: -0.90 (0.48), residues: 111 loop : -0.61 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 102 HIS 0.004 0.001 HIS 2 320 PHE 0.022 0.001 PHE C 599 TYR 0.016 0.001 TYR 2 412 ARG 0.008 0.000 ARG A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2962 Ramachandran restraints generated. 1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: 2 73 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6992 (t80) REVERT: 2 155 MET cc_start: 0.7246 (tpt) cc_final: 0.6885 (tpt) REVERT: 2 222 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6873 (mt) REVERT: 2 395 TYR cc_start: 0.8345 (m-10) cc_final: 0.8107 (m-10) REVERT: A 50 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7310 (ttm110) REVERT: A 82 MET cc_start: 0.7625 (ppp) cc_final: 0.7162 (ptp) REVERT: C 805 LEU cc_start: 0.8211 (tt) cc_final: 0.7904 (mp) REVERT: C 842 MET cc_start: 0.7258 (mtp) cc_final: 0.6765 (mtp) REVERT: T 141 MET cc_start: 0.6454 (mmt) cc_final: 0.6115 (mmt) REVERT: T 241 MET cc_start: 0.8034 (mtp) cc_final: 0.7711 (mtt) REVERT: T 247 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7933 (p0) REVERT: T 357 ARG cc_start: 0.7543 (mtp85) cc_final: 0.6798 (mmp80) outliers start: 24 outliers final: 20 residues processed: 145 average time/residue: 0.2395 time to fit residues: 52.4663 Evaluate side-chains 150 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 70 MET Chi-restraints excluded: chain 2 residue 73 TYR Chi-restraints excluded: chain 2 residue 130 ILE Chi-restraints excluded: chain 2 residue 222 ILE Chi-restraints excluded: chain 2 residue 303 ASN Chi-restraints excluded: chain 2 residue 339 ASN Chi-restraints excluded: chain 2 residue 428 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 152 ASN Chi-restraints excluded: chain T residue 247 ASN Chi-restraints excluded: chain T residue 261 SER Chi-restraints excluded: chain T residue 342 VAL Chi-restraints excluded: chain T residue 353 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 190 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 = 0.4128 r_free = 0.4128 target = 0.191686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137217 restraints weight = 12223.107| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.38 r_work: 0.3336 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12638 Z= 0.225 Angle : 0.527 16.401 17122 Z= 0.262 Chirality : 0.039 0.145 1928 Planarity : 0.004 0.057 2118 Dihedral : 11.179 167.545 1924 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 1.58 % Allowed : 11.38 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.26 (0.22), residues: 1481 helix: 1.94 (0.18), residues: 855 sheet: -0.90 (0.48), residues: 111 loop : -0.62 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP T 102 HIS 0.005 0.001 HIS 2 320 PHE 0.022 0.001 PHE C 599 TYR 0.015 0.001 TYR 2 412 ARG 0.007 0.000 ARG A 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2718.85 seconds wall clock time: 50 minutes 27.01 seconds (3027.01 seconds total)