Starting phenix.real_space_refine on Wed Feb 14 21:23:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3q_10094/02_2024/6s3q_10094.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3q_10094/02_2024/6s3q_10094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3q_10094/02_2024/6s3q_10094.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3q_10094/02_2024/6s3q_10094.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3q_10094/02_2024/6s3q_10094.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s3q_10094/02_2024/6s3q_10094.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 69 5.16 5 C 6816 2.51 5 N 1563 2.21 5 O 1827 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3241 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3241 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3241 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {'7O9': 1, 'PC1': 5, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {'7O9': 1, 'PC1': 5, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {'7O9': 1, 'PC1': 5, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 6.08, per 1000 atoms: 0.59 Number of scatterers: 10290 At special positions: 0 Unit cell: (116.202, 117.288, 89.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 6 15.00 F 9 9.00 O 1827 8.00 N 1563 7.00 C 6816 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: 3.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 76.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 19 through 40 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.828A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 removed outlier: 4.091A pdb=" N MET A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 117 removed outlier: 4.002A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 4.028A pdb=" N ALA A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.948A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 4.073A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 297 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.603A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.569A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.630A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.558A pdb=" N ALA A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.547A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 removed outlier: 3.618A pdb=" N LEU A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.878A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 433 through 441 removed outlier: 4.387A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 466 removed outlier: 3.855A pdb=" N THR A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 465 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.893A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 19 through 40 Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.828A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 removed outlier: 4.092A pdb=" N MET B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 117 removed outlier: 4.002A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 148 removed outlier: 4.028A pdb=" N ALA B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 229 Processing helix chain 'B' and resid 233 through 270 removed outlier: 3.948A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 4.072A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 297 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.603A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.569A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.631A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.558A pdb=" N ALA B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 403 removed outlier: 3.547A pdb=" N ILE B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 425 removed outlier: 3.618A pdb=" N LEU B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.876A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 433 through 441 removed outlier: 4.386A pdb=" N VAL B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 466 removed outlier: 3.854A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 3.894A pdb=" N GLU B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 19 through 40 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.828A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 86 removed outlier: 4.092A pdb=" N MET C 75 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 117 removed outlier: 4.002A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 148 removed outlier: 4.028A pdb=" N ALA C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'C' and resid 233 through 270 removed outlier: 3.948A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 4.072A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 297 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.603A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.568A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.630A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.557A pdb=" N ALA C 371 " --> pdb=" O MET C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 403 removed outlier: 3.548A pdb=" N ILE C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 425 removed outlier: 3.618A pdb=" N LEU C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.877A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 441 removed outlier: 4.388A pdb=" N VAL C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 466 removed outlier: 3.854A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 465 " --> pdb=" O ILE C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 476 removed outlier: 3.893A pdb=" N GLU C 471 " --> pdb=" O LYS C 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 168 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 168 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 168 651 hydrogen bonds defined for protein. 1944 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: 2.58 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1656 1.32 - 1.44: 2361 1.44 - 1.56: 6273 1.56 - 1.68: 15 1.68 - 1.80: 123 Bond restraints: 10428 Sorted by residual: bond pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 1.205 1.341 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C21 PC1 C 506 " pdb=" O22 PC1 C 506 " ideal model delta sigma weight residual 1.205 1.341 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C21 PC1 A 605 " pdb=" O22 PC1 A 605 " ideal model delta sigma weight residual 1.205 1.341 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C21 PC1 A 605 " pdb=" O21 PC1 A 605 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C21 PC1 B 506 " pdb=" O21 PC1 B 506 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.00e-02 2.50e+03 4.22e+01 ... (remaining 10423 not shown) Histogram of bond angle deviations from ideal: 97.42 - 104.74: 177 104.74 - 112.05: 5036 112.05 - 119.37: 4054 119.37 - 126.68: 4746 126.68 - 133.99: 75 Bond angle restraints: 14088 Sorted by residual: angle pdb=" C22 PC1 A 605 " pdb=" C21 PC1 A 605 " pdb=" O22 PC1 A 605 " ideal model delta sigma weight residual 125.37 111.22 14.15 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C22 PC1 B 506 " pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 125.37 111.23 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C22 PC1 C 506 " pdb=" C21 PC1 C 506 " pdb=" O22 PC1 C 506 " ideal model delta sigma weight residual 125.37 111.24 14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C22 PC1 B 506 " pdb=" C21 PC1 B 506 " pdb=" O21 PC1 B 506 " ideal model delta sigma weight residual 111.12 124.87 -13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C22 PC1 C 506 " pdb=" C21 PC1 C 506 " pdb=" O21 PC1 C 506 " ideal model delta sigma weight residual 111.12 124.83 -13.71 3.00e+00 1.11e-01 2.09e+01 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5834 17.59 - 35.17: 511 35.17 - 52.76: 105 52.76 - 70.35: 30 70.35 - 87.94: 6 Dihedral angle restraints: 6486 sinusoidal: 2781 harmonic: 3705 Sorted by residual: dihedral pdb=" CA ILE B 391 " pdb=" C ILE B 391 " pdb=" N GLY B 392 " pdb=" CA GLY B 392 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLU B 48 " pdb=" C GLU B 48 " pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLU C 48 " pdb=" C GLU C 48 " pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1161 0.054 - 0.107: 440 0.107 - 0.161: 123 0.161 - 0.214: 16 0.214 - 0.268: 6 Chirality restraints: 1746 Sorted by residual: chirality pdb=" C1 7O9 B 502 " pdb=" C 7O9 B 502 " pdb=" C2 7O9 B 502 " pdb=" N1 7O9 B 502 " both_signs ideal model delta sigma weight residual False 2.37 2.64 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 7O9 C 502 " pdb=" C 7O9 C 502 " pdb=" C2 7O9 C 502 " pdb=" N1 7O9 C 502 " both_signs ideal model delta sigma weight residual False 2.37 2.64 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 7O9 A 601 " pdb=" C 7O9 A 601 " pdb=" C2 7O9 A 601 " pdb=" N1 7O9 A 601 " both_signs ideal model delta sigma weight residual False 2.37 2.64 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1743 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 275 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" CG ASP B 275 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP B 275 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 275 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 275 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" CG ASP A 275 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP A 275 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 275 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 275 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" CG ASP C 275 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 275 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 275 " 0.013 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3679 2.89 - 3.39: 9647 3.39 - 3.89: 15933 3.89 - 4.40: 18403 4.40 - 4.90: 32524 Nonbonded interactions: 80186 Sorted by model distance: nonbonded pdb=" NH1 ARG C 447 " pdb=" O2 7O9 C 502 " model vdw 2.383 2.520 nonbonded pdb=" NH1 ARG B 447 " pdb=" O2 7O9 B 502 " model vdw 2.383 2.520 nonbonded pdb=" NH1 ARG A 447 " pdb=" O2 7O9 A 601 " model vdw 2.384 2.520 nonbonded pdb=" O THR B 138 " pdb=" OG1 THR B 138 " model vdw 2.395 2.440 nonbonded pdb=" O THR A 138 " pdb=" OG1 THR A 138 " model vdw 2.395 2.440 ... (remaining 80181 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 476 or (resid 604 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name O21 or name O22)) or resid 605 or (resid 607 an \ d (name C1 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ C3B or name C3C or name O21 or name O31 or name O32)))) selection = (chain 'B' and (resid 10 through 476 or (resid 504 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name O21 or name O22)) or (resid 505 and (name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C2A or name C2B or name C2C or name C2D or name O21 or na \ me O22)) or resid 507)) selection = (chain 'C' and (resid 10 through 476 or (resid 504 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name O21 or name O22)) or (resid 505 and (name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C2A or name C2B or name C2C or name C2D or name O21 or na \ me O22)) or resid 507)) } 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: 0.630 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: 2.410 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.280 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.012 0.136 10428 Z= 0.753 Angle : 1.105 14.154 14088 Z= 0.581 Chirality : 0.061 0.268 1746 Planarity : 0.007 0.050 1677 Dihedral : 14.478 87.937 4092 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.44 % Rotamer: Outliers : 0.57 % Allowed : 7.16 % Favored : 92.26 % 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: -4.53 (0.16), residues: 1272 helix: -2.83 (0.11), residues: 915 sheet: None (None), residues: 0 loop : -2.90 (0.26), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 19 HIS 0.001 0.001 HIS C 296 PHE 0.025 0.003 PHE A 159 TYR 0.028 0.003 TYR B 373 ARG 0.004 0.001 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.239 Fit side-chains REVERT: A 60 MET cc_start: 0.8678 (mmt) cc_final: 0.8205 (mmt) REVERT: A 232 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7970 (mtmt) REVERT: A 255 MET cc_start: 0.8939 (mmt) cc_final: 0.8619 (mmt) REVERT: A 315 ARG cc_start: 0.7824 (mmt90) cc_final: 0.6839 (ttt90) REVERT: B 60 MET cc_start: 0.8727 (mmt) cc_final: 0.8394 (mmt) REVERT: B 315 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7012 (ttt90) REVERT: C 75 MET cc_start: 0.8841 (mmm) cc_final: 0.8477 (mmm) REVERT: C 90 ILE cc_start: 0.8899 (tt) cc_final: 0.8670 (tt) REVERT: C 232 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8075 (mtmt) REVERT: C 255 MET cc_start: 0.9045 (mmt) cc_final: 0.8716 (mmm) REVERT: C 315 ARG cc_start: 0.7789 (mmt90) cc_final: 0.7500 (mmt90) outliers start: 6 outliers final: 0 residues processed: 144 average time/residue: 0.2321 time to fit residues: 48.1185 Evaluate side-chains 112 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 347 ASN A 366 ASN A 413 GLN B 322 GLN B 366 ASN B 413 GLN C 322 GLN C 366 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10428 Z= 0.235 Angle : 0.579 5.775 14088 Z= 0.304 Chirality : 0.040 0.155 1746 Planarity : 0.004 0.035 1677 Dihedral : 10.198 69.418 1929 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.76 % Allowed : 12.80 % Favored : 86.44 % 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: -1.56 (0.22), residues: 1272 helix: -0.54 (0.17), residues: 930 sheet: -2.37 (0.65), residues: 60 loop : -1.90 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.001 0.000 HIS A 296 PHE 0.021 0.002 PHE A 357 TYR 0.011 0.001 TYR C 257 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.051 Fit side-chains REVERT: A 60 MET cc_start: 0.8672 (mmt) cc_final: 0.8301 (mmt) REVERT: A 232 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8025 (mtmt) REVERT: A 315 ARG cc_start: 0.7745 (mmt90) cc_final: 0.6823 (ttt90) REVERT: B 60 MET cc_start: 0.8721 (mmt) cc_final: 0.8411 (mmt) REVERT: B 231 GLU cc_start: 0.8095 (tp30) cc_final: 0.7771 (tp30) REVERT: B 255 MET cc_start: 0.8921 (mmt) cc_final: 0.8215 (mmt) REVERT: B 315 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7089 (ttt90) REVERT: C 75 MET cc_start: 0.8655 (mmm) cc_final: 0.8354 (mmm) REVERT: C 90 ILE cc_start: 0.8866 (tt) cc_final: 0.8611 (tt) REVERT: C 232 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8152 (mtmt) REVERT: C 255 MET cc_start: 0.8871 (mmt) cc_final: 0.8565 (mmm) REVERT: C 286 MET cc_start: 0.7311 (mtm) cc_final: 0.7002 (mtp) REVERT: C 315 ARG cc_start: 0.7743 (mmt90) cc_final: 0.7456 (mmt90) REVERT: C 449 MET cc_start: 0.7683 (ttp) cc_final: 0.7441 (ttp) outliers start: 8 outliers final: 7 residues processed: 138 average time/residue: 0.1859 time to fit residues: 38.6532 Evaluate side-chains 120 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 271 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 104 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 94 optimal weight: 0.0000 overall best weight: 0.5424 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10428 Z= 0.135 Angle : 0.504 5.552 14088 Z= 0.258 Chirality : 0.038 0.124 1746 Planarity : 0.003 0.030 1677 Dihedral : 9.232 68.119 1929 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.67 % Allowed : 14.90 % Favored : 84.43 % 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: -0.22 (0.25), residues: 1272 helix: 0.51 (0.18), residues: 921 sheet: -2.05 (0.68), residues: 60 loop : -1.55 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.008 0.001 PHE A 357 TYR 0.011 0.001 TYR C 257 ARG 0.001 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.160 Fit side-chains REVERT: A 60 MET cc_start: 0.8525 (mmt) cc_final: 0.8246 (mmt) REVERT: A 232 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8147 (mtmt) REVERT: A 255 MET cc_start: 0.8825 (mmt) cc_final: 0.8136 (mmt) REVERT: A 309 VAL cc_start: 0.9008 (t) cc_final: 0.8803 (m) REVERT: A 315 ARG cc_start: 0.7714 (mmt90) cc_final: 0.6799 (ttt90) REVERT: B 60 MET cc_start: 0.8606 (mmt) cc_final: 0.8252 (mmt) REVERT: B 231 GLU cc_start: 0.8137 (tp30) cc_final: 0.7856 (tp30) REVERT: B 255 MET cc_start: 0.8835 (mmt) cc_final: 0.8231 (mmt) REVERT: B 286 MET cc_start: 0.7150 (mtt) cc_final: 0.6805 (mtp) REVERT: B 315 ARG cc_start: 0.7851 (mmt90) cc_final: 0.7048 (ttt90) REVERT: C 90 ILE cc_start: 0.8746 (tt) cc_final: 0.8450 (tt) REVERT: C 231 GLU cc_start: 0.8039 (tp30) cc_final: 0.7610 (tp30) REVERT: C 232 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8269 (mtmt) REVERT: C 255 MET cc_start: 0.8806 (mmt) cc_final: 0.8556 (mmm) REVERT: C 315 ARG cc_start: 0.7664 (mmt90) cc_final: 0.7368 (mmt90) REVERT: C 343 CYS cc_start: 0.8650 (m) cc_final: 0.8322 (m) REVERT: C 449 MET cc_start: 0.7610 (ttp) cc_final: 0.7370 (ttp) outliers start: 7 outliers final: 5 residues processed: 144 average time/residue: 0.1847 time to fit residues: 40.3536 Evaluate side-chains 124 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.0670 chunk 124 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10428 Z= 0.166 Angle : 0.501 5.495 14088 Z= 0.255 Chirality : 0.038 0.132 1746 Planarity : 0.003 0.030 1677 Dihedral : 9.082 66.074 1929 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 15.47 % Favored : 83.00 % 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: 0.24 (0.25), residues: 1272 helix: 0.83 (0.18), residues: 924 sheet: -1.98 (0.67), residues: 60 loop : -1.35 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE B 159 TYR 0.012 0.001 TYR B 257 ARG 0.001 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.998 Fit side-chains REVERT: A 60 MET cc_start: 0.8614 (mmt) cc_final: 0.8409 (mmt) REVERT: A 255 MET cc_start: 0.8822 (mmt) cc_final: 0.8215 (mmt) REVERT: A 309 VAL cc_start: 0.8945 (t) cc_final: 0.8730 (m) REVERT: A 315 ARG cc_start: 0.7806 (mmt90) cc_final: 0.6865 (ttt90) REVERT: B 60 MET cc_start: 0.8544 (mmt) cc_final: 0.8228 (mmt) REVERT: B 235 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 255 MET cc_start: 0.8849 (mmt) cc_final: 0.8245 (mmt) REVERT: B 315 ARG cc_start: 0.7757 (mmt90) cc_final: 0.6955 (ttt90) REVERT: C 90 ILE cc_start: 0.8755 (tt) cc_final: 0.8479 (tt) REVERT: C 232 LYS cc_start: 0.8494 (mtmt) cc_final: 0.8255 (mtmt) REVERT: C 255 MET cc_start: 0.8845 (mmt) cc_final: 0.8579 (mmm) REVERT: C 315 ARG cc_start: 0.7632 (mmt90) cc_final: 0.7318 (mmt90) REVERT: C 328 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8433 (mp) REVERT: C 343 CYS cc_start: 0.8592 (m) cc_final: 0.8274 (m) REVERT: C 449 MET cc_start: 0.7617 (ttp) cc_final: 0.7383 (ttp) outliers start: 16 outliers final: 10 residues processed: 146 average time/residue: 0.2080 time to fit residues: 46.6140 Evaluate side-chains 138 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10428 Z= 0.147 Angle : 0.498 9.227 14088 Z= 0.251 Chirality : 0.038 0.134 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.850 65.739 1929 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.91 % Allowed : 15.76 % Favored : 82.33 % 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: 0.66 (0.25), residues: 1272 helix: 1.15 (0.18), residues: 921 sheet: -1.89 (0.67), residues: 60 loop : -1.20 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.009 0.001 PHE B 159 TYR 0.012 0.001 TYR B 257 ARG 0.001 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.335 Fit side-chains REVERT: A 235 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7949 (tp) REVERT: A 315 ARG cc_start: 0.7746 (mmt90) cc_final: 0.6791 (ttt90) REVERT: B 60 MET cc_start: 0.8509 (mmt) cc_final: 0.8205 (mmt) REVERT: B 235 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8106 (tp) REVERT: B 255 MET cc_start: 0.8845 (mmt) cc_final: 0.8223 (mmt) REVERT: B 315 ARG cc_start: 0.7657 (mmt90) cc_final: 0.6848 (ttt90) REVERT: C 90 ILE cc_start: 0.8668 (tt) cc_final: 0.8394 (tt) REVERT: C 232 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8211 (mtmt) REVERT: C 235 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7993 (tp) REVERT: C 255 MET cc_start: 0.8840 (mmt) cc_final: 0.8618 (mmm) REVERT: C 315 ARG cc_start: 0.7604 (mmt90) cc_final: 0.7280 (mmt90) REVERT: C 328 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8356 (mp) outliers start: 20 outliers final: 15 residues processed: 153 average time/residue: 0.1981 time to fit residues: 46.3830 Evaluate side-chains 145 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10428 Z= 0.143 Angle : 0.486 6.836 14088 Z= 0.246 Chirality : 0.038 0.138 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.654 64.534 1929 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.10 % Allowed : 15.76 % Favored : 82.14 % 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: 0.94 (0.25), residues: 1272 helix: 1.36 (0.18), residues: 927 sheet: -1.65 (0.68), residues: 60 loop : -1.18 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.009 0.001 PHE B 159 TYR 0.009 0.001 TYR B 257 ARG 0.001 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.166 Fit side-chains REVERT: A 235 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 258 MET cc_start: 0.8128 (tmm) cc_final: 0.7909 (tmm) REVERT: A 315 ARG cc_start: 0.7686 (mmt90) cc_final: 0.6783 (ttt90) REVERT: B 60 MET cc_start: 0.8376 (mmt) cc_final: 0.8074 (mmt) REVERT: B 235 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 255 MET cc_start: 0.8853 (mmt) cc_final: 0.8212 (mmt) REVERT: B 315 ARG cc_start: 0.7746 (mmt90) cc_final: 0.6994 (ttt90) REVERT: C 90 ILE cc_start: 0.8621 (tt) cc_final: 0.8367 (tt) REVERT: C 232 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8260 (mtmt) REVERT: C 235 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8022 (tp) REVERT: C 255 MET cc_start: 0.8838 (mmt) cc_final: 0.8618 (mmm) REVERT: C 286 MET cc_start: 0.7330 (mtp) cc_final: 0.7012 (mtp) REVERT: C 315 ARG cc_start: 0.7553 (mmt90) cc_final: 0.7222 (mmt90) REVERT: C 328 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8252 (mp) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.1803 time to fit residues: 41.5836 Evaluate side-chains 149 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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: 0.8086 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10428 Z= 0.153 Angle : 0.488 6.533 14088 Z= 0.247 Chirality : 0.038 0.144 1746 Planarity : 0.003 0.027 1677 Dihedral : 8.558 65.702 1929 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.29 % Allowed : 16.43 % Favored : 81.28 % 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: 1.06 (0.25), residues: 1272 helix: 1.43 (0.18), residues: 930 sheet: -1.56 (0.69), residues: 60 loop : -1.14 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.010 0.001 PHE B 159 TYR 0.010 0.001 TYR B 257 ARG 0.001 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.163 Fit side-chains REVERT: A 235 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7912 (tp) REVERT: A 315 ARG cc_start: 0.7675 (mmt90) cc_final: 0.6754 (ttt90) REVERT: A 442 LEU cc_start: 0.9300 (mt) cc_final: 0.8936 (mt) REVERT: B 60 MET cc_start: 0.8394 (mmt) cc_final: 0.8100 (mmt) REVERT: B 235 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8102 (tp) REVERT: B 255 MET cc_start: 0.8848 (mmt) cc_final: 0.8224 (mmt) REVERT: B 315 ARG cc_start: 0.7767 (mmt90) cc_final: 0.7000 (ttt90) REVERT: C 90 ILE cc_start: 0.8595 (tt) cc_final: 0.8352 (tt) REVERT: C 232 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8194 (mtmt) REVERT: C 235 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8062 (tp) REVERT: C 255 MET cc_start: 0.8844 (mmt) cc_final: 0.8620 (mmm) REVERT: C 286 MET cc_start: 0.7246 (mtp) cc_final: 0.6923 (mtp) REVERT: C 315 ARG cc_start: 0.7558 (mmt90) cc_final: 0.7210 (mmt90) REVERT: C 328 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8167 (mp) outliers start: 24 outliers final: 19 residues processed: 154 average time/residue: 0.1812 time to fit residues: 42.6444 Evaluate side-chains 158 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10428 Z= 0.154 Angle : 0.500 10.891 14088 Z= 0.251 Chirality : 0.039 0.143 1746 Planarity : 0.003 0.027 1677 Dihedral : 8.456 65.345 1929 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.58 % Allowed : 16.43 % Favored : 80.99 % 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: 1.21 (0.25), residues: 1272 helix: 1.54 (0.18), residues: 930 sheet: -1.36 (0.71), residues: 60 loop : -1.12 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE B 159 TYR 0.009 0.001 TYR B 257 ARG 0.001 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.227 Fit side-chains REVERT: A 235 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7963 (tp) REVERT: A 315 ARG cc_start: 0.7674 (mmt90) cc_final: 0.6760 (ttt90) REVERT: A 442 LEU cc_start: 0.9300 (mt) cc_final: 0.8941 (mt) REVERT: B 60 MET cc_start: 0.8382 (mmt) cc_final: 0.8099 (mmt) REVERT: B 235 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8095 (tp) REVERT: B 255 MET cc_start: 0.8846 (mmt) cc_final: 0.8237 (mmt) REVERT: B 315 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7014 (ttt90) REVERT: C 90 ILE cc_start: 0.8590 (tt) cc_final: 0.8348 (tt) REVERT: C 232 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8178 (mtmt) REVERT: C 235 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8052 (tp) REVERT: C 255 MET cc_start: 0.8850 (mmt) cc_final: 0.8624 (mmm) REVERT: C 286 MET cc_start: 0.7273 (mtp) cc_final: 0.6949 (mtp) REVERT: C 315 ARG cc_start: 0.7559 (mmt90) cc_final: 0.7205 (mmt90) REVERT: C 328 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8164 (mp) REVERT: C 433 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8284 (t) outliers start: 27 outliers final: 21 residues processed: 158 average time/residue: 0.1798 time to fit residues: 43.3064 Evaluate side-chains 164 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8100 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10428 Z= 0.176 Angle : 0.513 10.722 14088 Z= 0.257 Chirality : 0.039 0.156 1746 Planarity : 0.003 0.027 1677 Dihedral : 8.449 65.530 1929 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.58 % Allowed : 16.43 % Favored : 80.99 % 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: 1.24 (0.25), residues: 1272 helix: 1.52 (0.18), residues: 936 sheet: -1.22 (0.72), residues: 60 loop : -1.03 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.012 0.001 PHE B 159 TYR 0.010 0.001 TYR B 257 ARG 0.001 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.286 Fit side-chains REVERT: A 235 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8009 (tp) REVERT: A 315 ARG cc_start: 0.7683 (mmt90) cc_final: 0.6772 (ttt90) REVERT: A 442 LEU cc_start: 0.9308 (mt) cc_final: 0.8977 (mt) REVERT: B 60 MET cc_start: 0.8440 (mmt) cc_final: 0.8145 (mmt) REVERT: B 235 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 255 MET cc_start: 0.8868 (mmt) cc_final: 0.8238 (mmt) REVERT: B 315 ARG cc_start: 0.7837 (mmt90) cc_final: 0.7038 (ttt90) REVERT: C 90 ILE cc_start: 0.8627 (tt) cc_final: 0.8369 (tt) REVERT: C 232 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8157 (mtmt) REVERT: C 235 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8086 (tp) REVERT: C 255 MET cc_start: 0.8856 (mmt) cc_final: 0.8623 (mmm) REVERT: C 286 MET cc_start: 0.7297 (mtp) cc_final: 0.6987 (mtp) REVERT: C 315 ARG cc_start: 0.7564 (mmt90) cc_final: 0.7205 (mmt90) REVERT: C 328 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8149 (mp) REVERT: C 433 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8307 (t) outliers start: 27 outliers final: 21 residues processed: 159 average time/residue: 0.1744 time to fit residues: 42.1405 Evaluate side-chains 160 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 109 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10428 Z= 0.192 Angle : 0.533 13.949 14088 Z= 0.266 Chirality : 0.039 0.154 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.499 64.715 1929 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.48 % Allowed : 16.62 % Favored : 80.90 % 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: 1.16 (0.25), residues: 1272 helix: 1.43 (0.18), residues: 945 sheet: -1.13 (0.73), residues: 60 loop : -1.01 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.013 0.001 PHE B 159 TYR 0.010 0.001 TYR B 257 ARG 0.001 0.000 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.024 Fit side-chains REVERT: A 235 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7987 (tp) REVERT: A 258 MET cc_start: 0.8146 (tmm) cc_final: 0.7902 (tmm) REVERT: A 315 ARG cc_start: 0.7692 (mmt90) cc_final: 0.6782 (ttt90) REVERT: B 60 MET cc_start: 0.8461 (mmt) cc_final: 0.8167 (mmt) REVERT: B 235 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8150 (tp) REVERT: B 255 MET cc_start: 0.8886 (mmt) cc_final: 0.8245 (mmt) REVERT: B 315 ARG cc_start: 0.7838 (mmt90) cc_final: 0.7000 (ttt90) REVERT: C 90 ILE cc_start: 0.8657 (tt) cc_final: 0.8392 (tt) REVERT: C 232 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8142 (mtmt) REVERT: C 235 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8168 (tp) REVERT: C 286 MET cc_start: 0.7317 (mtp) cc_final: 0.7003 (mtp) REVERT: C 315 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7208 (mmt90) REVERT: C 328 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8206 (mp) outliers start: 26 outliers final: 22 residues processed: 157 average time/residue: 0.1800 time to fit residues: 42.9591 Evaluate side-chains 164 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 439 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.129163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.090970 restraints weight = 11510.765| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.59 r_work: 0.2672 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10428 Z= 0.231 Angle : 0.555 13.990 14088 Z= 0.278 Chirality : 0.040 0.159 1746 Planarity : 0.003 0.027 1677 Dihedral : 8.792 63.023 1929 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.58 % Allowed : 16.14 % Favored : 81.28 % 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 (0.25), residues: 1272 helix: 1.36 (0.18), residues: 942 sheet: -0.97 (0.69), residues: 66 loop : -0.98 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.016 0.002 PHE B 159 TYR 0.010 0.001 TYR B 257 ARG 0.001 0.000 ARG B 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.72 seconds wall clock time: 38 minutes 54.92 seconds (2334.92 seconds total)