Starting phenix.real_space_refine on Thu Jul 2 16:47:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srp_40737/07_2026/8srp_40737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srp_40737/07_2026/8srp_40737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8srp_40737/07_2026/8srp_40737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srp_40737/07_2026/8srp_40737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srp_40737/07_2026/8srp_40737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srp_40737/07_2026/8srp_40737.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.053 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 212 5.49 5 S 6 5.16 5 C 5333 2.51 5 N 1760 2.21 5 O 2205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9516 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 664 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "I" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "N" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1108 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain: "M" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1103 Classifications: {'DNA': 54} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 53} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1087 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "K" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1083 Classifications: {'DNA': 53} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 52} Chain: "J" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "H" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 424 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 231 Chain: "G" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "F" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 424 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 456 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 231 Chain: "E" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 419 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 314 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 5, 'PHE:plan': 7, 'HIS:plan': 5, 'ASN:plan1': 5, 'ARG:plan': 8, 'TRP:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 628 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 640 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 679 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 82} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 1.72, per 1000 atoms: 0.18 Number of scatterers: 9516 At special positions: 0 Unit cell: (79.336, 86.932, 181.46, 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 6 16.00 P 212 15.00 O 2205 8.00 N 1760 7.00 C 5333 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 - 3.00 Amino acid : True - 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: 0.65 Conformation dependent library (CDL) restraints added in 192.4 milliseconds 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 51.6% alpha, 8.7% beta 91 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.950A pdb=" N PHE A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 334' Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 359 through 371 removed outlier: 3.568A pdb=" N PHE A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 4.982A pdb=" N ILE A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 334 Processing helix chain 'I' and resid 341 through 351 Processing helix chain 'I' and resid 359 through 371 Processing helix chain 'I' and resid 379 through 392 removed outlier: 3.696A pdb=" N ALA I 384 " --> pdb=" O THR I 380 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE I 385 " --> pdb=" O TRP I 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 334 Processing helix chain 'J' and resid 341 through 351 Processing helix chain 'J' and resid 359 through 371 removed outlier: 3.719A pdb=" N HIS J 365 " --> pdb=" O ASN J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 392 removed outlier: 3.812A pdb=" N ALA J 384 " --> pdb=" O THR J 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 334 Processing helix chain 'H' and resid 341 through 350 Processing helix chain 'H' and resid 359 through 371 Processing helix chain 'H' and resid 379 through 392 removed outlier: 3.727A pdb=" N ALA H 384 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE H 385 " --> pdb=" O TRP H 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 351 Processing helix chain 'G' and resid 359 through 371 removed outlier: 3.639A pdb=" N HIS G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 392 removed outlier: 3.807A pdb=" N ALA G 384 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE G 385 " --> pdb=" O TRP G 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 333 Processing helix chain 'F' and resid 341 through 351 removed outlier: 3.607A pdb=" N ARG F 347 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP F 348 " --> pdb=" O THR F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 371 removed outlier: 3.621A pdb=" N HIS F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 392 removed outlier: 3.918A pdb=" N ALA F 384 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'E' and resid 341 through 351 Processing helix chain 'E' and resid 359 through 371 removed outlier: 3.576A pdb=" N PHE E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR E 368 " --> pdb=" O TYR E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.698A pdb=" N ASN E 376 " --> pdb=" O TYR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 392 removed outlier: 3.943A pdb=" N ALA E 384 " --> pdb=" O THR E 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 334 Processing helix chain 'D' and resid 341 through 351 Processing helix chain 'D' and resid 359 through 371 Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.751A pdb=" N ALA D 384 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.702A pdb=" N HIS C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.798A pdb=" N ALA C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 359 through 371 removed outlier: 3.581A pdb=" N PHE B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.964A pdb=" N ALA B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS B 392 " --> pdb=" O ASN B 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 399 Processing sheet with id=AA2, first strand: chain 'I' and resid 396 through 399 Processing sheet with id=AA3, first strand: chain 'J' and resid 396 through 399 Processing sheet with id=AA4, first strand: chain 'H' and resid 396 through 400 removed outlier: 3.542A pdb=" N THR H 407 " --> pdb=" O VAL H 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 357 through 358 Processing sheet with id=AA6, first strand: chain 'F' and resid 357 through 359 Processing sheet with id=AA7, first strand: chain 'E' and resid 396 through 400 removed outlier: 3.770A pdb=" N VAL E 396 " --> pdb=" O THR E 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 395 through 399 Processing sheet with id=AA9, first strand: chain 'C' and resid 395 through 399 Processing sheet with id=AB1, first strand: chain 'B' and resid 396 through 399 293 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 203 hydrogen bonds 402 hydrogen bond angles 0 basepair planarities 91 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1741 1.33 - 1.45: 3381 1.45 - 1.57: 4582 1.57 - 1.69: 423 1.69 - 1.81: 8 Bond restraints: 10135 Sorted by residual: bond pdb=" C3' DT M 16 " pdb=" C2' DT M 16 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DT K 38 " pdb=" C2' DT K 38 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DC N 44 " pdb=" C2' DC N 44 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DT K 46 " pdb=" C2' DT K 46 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DA L 15 " pdb=" C2' DA L 15 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 ... (remaining 10130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 14746 3.23 - 6.47: 46 6.47 - 9.70: 2 9.70 - 12.94: 1 12.94 - 16.17: 2 Bond angle restraints: 14797 Sorted by residual: angle pdb=" CA PRO C 354 " pdb=" N PRO C 354 " pdb=" CD PRO C 354 " ideal model delta sigma weight residual 112.00 95.83 16.17 1.40e+00 5.10e-01 1.33e+02 angle pdb=" O4' DA L 43 " pdb=" C1' DA L 43 " pdb=" N9 DA L 43 " ideal model delta sigma weight residual 108.00 111.70 -3.70 7.00e-01 2.04e+00 2.79e+01 angle pdb=" N3 DT K 18 " pdb=" C4 DT K 18 " pdb=" O4 DT K 18 " ideal model delta sigma weight residual 119.90 122.89 -2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" O4' DA L 21 " pdb=" C4' DA L 21 " pdb=" C3' DA L 21 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.25e+01 angle pdb=" O4' DT K 24 " pdb=" C4' DT K 24 " pdb=" C3' DT K 24 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.14e+01 ... (remaining 14792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.47: 4172 27.47 - 54.94: 1093 54.94 - 82.41: 202 82.41 - 109.88: 5 109.88 - 137.36: 5 Dihedral angle restraints: 5477 sinusoidal: 2944 harmonic: 2533 Sorted by residual: dihedral pdb=" CA ALA C 353 " pdb=" C ALA C 353 " pdb=" N PRO C 354 " pdb=" CA PRO C 354 " ideal model delta harmonic sigma weight residual 180.00 147.01 32.99 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" C4' DT M 2 " pdb=" C3' DT M 2 " pdb=" O3' DT M 2 " pdb=" P DG M 3 " ideal model delta sinusoidal sigma weight residual 220.00 82.64 137.36 1 3.50e+01 8.16e-04 1.36e+01 dihedral pdb=" C4' DT K 10 " pdb=" C3' DT K 10 " pdb=" O3' DT K 10 " pdb=" P DG K 11 " ideal model delta sinusoidal sigma weight residual 220.00 88.55 131.45 1 3.50e+01 8.16e-04 1.30e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 855 0.028 - 0.056: 570 0.056 - 0.083: 183 0.083 - 0.111: 129 0.111 - 0.139: 18 Chirality restraints: 1755 Sorted by residual: chirality pdb=" C3' DA L 31 " pdb=" C4' DA L 31 " pdb=" O3' DA L 31 " pdb=" C2' DA L 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" C3' DT K 10 " pdb=" C4' DT K 10 " pdb=" O3' DT K 10 " pdb=" C2' DT K 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" C3' DT M 17 " pdb=" C4' DT M 17 " pdb=" O3' DT M 17 " pdb=" C2' DT M 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1752 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 353 " 0.143 5.00e-02 4.00e+02 2.01e-01 6.46e+01 pdb=" N PRO C 354 " -0.347 5.00e-02 4.00e+02 pdb=" CA PRO C 354 " 0.112 5.00e-02 4.00e+02 pdb=" CD PRO C 354 " 0.091 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 330 " -0.010 2.00e-02 2.50e+03 1.27e-02 3.24e+00 pdb=" CG TYR B 330 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 330 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 330 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 330 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 330 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 330 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 330 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 22 " -0.014 2.00e-02 2.50e+03 8.29e-03 1.89e+00 pdb=" N9 DA N 22 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA N 22 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA N 22 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA N 22 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA N 22 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA N 22 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA N 22 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA N 22 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DA N 22 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA N 22 " 0.005 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2404 2.81 - 3.33: 8954 3.33 - 3.85: 18244 3.85 - 4.38: 19300 4.38 - 4.90: 26904 Nonbonded interactions: 75806 Sorted by model distance: nonbonded pdb=" NE1 TRP A 406 " pdb=" OP2 DT K 18 " model vdw 2.286 3.120 nonbonded pdb=" NH2 ARG A 397 " pdb=" OP1 DT K 18 " model vdw 2.421 3.120 nonbonded pdb=" N GLU B 399 " pdb=" OE1 GLU B 399 " model vdw 2.422 3.120 nonbonded pdb=" O5' DG M 27 " pdb=" NH2 ARG B 397 " model vdw 2.448 3.120 nonbonded pdb=" O THR A 368 " pdb=" NE ARG A 375 " model vdw 2.466 3.120 ... (remaining 75801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 329 through 402 and (name N or name CA or name C or name \ O or name CB )) or (resid 403 through 411 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'B' and ((resid 329 through 402 and (name N or name CA or name C or name \ O or name CB )) or (resid 403 through 411 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'C' and ((resid 329 through 402 and (name N or name CA or name C or name \ O or name CB )) or (resid 403 through 411 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'D' and ((resid 329 through 402 and (name N or name CA or name C or name \ O or name CB )) or (resid 403 through 411 and (name N or name CA or name C or na \ me O or name CB )))) selection = (chain 'E' and resid 329 through 411) selection = (chain 'F' and resid 329 through 411) selection = (chain 'G' and resid 329 through 411) selection = (chain 'H' and resid 329 through 411) selection = (chain 'I' and resid 329 through 411) selection = (chain 'J' and resid 329 through 411) } ncs_group { reference = chain 'K' selection = (chain 'M' and resid 1 through 53) } ncs_group { reference = chain 'L' selection = (chain 'N' and resid 2 through 54) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.530 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 10135 Z= 0.517 Angle : 0.813 16.173 14797 Z= 0.721 Chirality : 0.044 0.139 1755 Planarity : 0.007 0.201 1186 Dihedral : 28.750 137.356 3799 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.47 % Allowed : 29.91 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.29), residues: 829 helix: -1.02 (0.24), residues: 444 sheet: -0.32 (0.44), residues: 122 loop : -0.83 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 358 TYR 0.031 0.002 TYR B 330 PHE 0.014 0.001 PHE A 340 TRP 0.012 0.001 TRP C 348 HIS 0.006 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.52 (10135) covalent geometry : angle 0.81280 / 0.72 (14797) hydrogen bonds : bond 0.19369 / 13.00 ( 496) hydrogen bonds : angle 7.28705 / 5.42 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.326 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.0767 time to fit residues: 8.7270 Evaluate side-chains 70 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 340 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.4684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 383 ASN ** 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 = 0.4231 r_free = 0.4231 target = 0.123417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.098947 restraints weight = 33955.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.099669 restraints weight = 22774.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.100000 restraints weight = 15524.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.100580 restraints weight = 13648.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.100495 restraints weight = 11659.103| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10135 Z= 0.191 Angle : 0.672 9.428 14797 Z= 0.416 Chirality : 0.042 0.209 1755 Planarity : 0.005 0.126 1186 Dihedral : 29.808 138.088 3330 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.67 % Allowed : 28.50 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.29), residues: 829 helix: -0.58 (0.24), residues: 426 sheet: -0.21 (0.44), residues: 122 loop : -1.15 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 369 TYR 0.019 0.002 TYR B 364 PHE 0.014 0.001 PHE A 340 TRP 0.010 0.001 TRP B 366 HIS 0.008 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.19 (10135) covalent geometry : angle 0.67217 / 0.42 (14797) hydrogen bonds : bond 0.06270 / 4.42 ( 496) hydrogen bonds : angle 5.27008 / 3.90 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7696 (ttt-90) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.0907 time to fit residues: 9.8001 Evaluate side-chains 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 336 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.119413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.094842 restraints weight = 35234.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.095173 restraints weight = 31011.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.096012 restraints weight = 23431.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.096003 restraints weight = 16883.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.096355 restraints weight = 16140.988| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 10135 Z= 0.403 Angle : 0.861 13.087 14797 Z= 0.505 Chirality : 0.052 0.242 1755 Planarity : 0.006 0.096 1186 Dihedral : 30.051 139.290 3328 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 8.41 % Allowed : 24.77 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.28), residues: 829 helix: -1.02 (0.23), residues: 430 sheet: -0.71 (0.43), residues: 122 loop : -1.60 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 386 TYR 0.018 0.003 TYR A 364 PHE 0.020 0.002 PHE C 395 TRP 0.020 0.002 TRP B 366 HIS 0.011 0.002 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00790 / 0.40 (10135) covalent geometry : angle 0.86137 / 0.51 (14797) hydrogen bonds : bond 0.09442 / 6.80 ( 496) hydrogen bonds : angle 5.56606 / 4.09 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.283 Fit side-chains REVERT: D 397 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7743 (ttt-90) outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.0713 time to fit residues: 8.5312 Evaluate side-chains 77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 398 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.0570 chunk 56 optimal weight: 9.9990 chunk 8 optimal weight: 30.0000 chunk 43 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 44 optimal weight: 40.0000 chunk 88 optimal weight: 0.7980 chunk 40 optimal weight: 40.0000 chunk 53 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.120293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.095698 restraints weight = 35961.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.095783 restraints weight = 32221.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.096844 restraints weight = 24235.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.096733 restraints weight = 17391.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.096957 restraints weight = 16711.149| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 10135 Z= 0.297 Angle : 0.764 11.505 14797 Z= 0.456 Chirality : 0.047 0.219 1755 Planarity : 0.006 0.087 1186 Dihedral : 30.065 142.059 3328 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 9.35 % Allowed : 27.10 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.29), residues: 829 helix: -0.77 (0.24), residues: 433 sheet: -1.01 (0.41), residues: 122 loop : -1.46 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 337 TYR 0.023 0.003 TYR B 373 PHE 0.016 0.002 PHE A 340 TRP 0.009 0.001 TRP B 366 HIS 0.010 0.002 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.30 (10135) covalent geometry : angle 0.76434 / 0.46 (14797) hydrogen bonds : bond 0.07496 / 5.50 ( 496) hydrogen bonds : angle 5.08946 / 3.75 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.260 Fit side-chains REVERT: D 397 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7823 (ttt-90) outliers start: 20 outliers final: 17 residues processed: 76 average time/residue: 0.0707 time to fit residues: 8.5869 Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 377 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 388 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.121195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.096971 restraints weight = 33933.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.098037 restraints weight = 23822.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.098479 restraints weight = 18258.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.098386 restraints weight = 14157.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.098682 restraints weight = 12233.354| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10135 Z= 0.213 Angle : 0.696 9.777 14797 Z= 0.421 Chirality : 0.043 0.193 1755 Planarity : 0.005 0.081 1186 Dihedral : 30.059 143.439 3328 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 8.41 % Allowed : 27.57 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.29), residues: 829 helix: -0.31 (0.25), residues: 429 sheet: -1.07 (0.40), residues: 122 loop : -1.25 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 337 TYR 0.020 0.003 TYR B 364 PHE 0.014 0.001 PHE A 340 TRP 0.010 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.21 (10135) covalent geometry : angle 0.69565 / 0.42 (14797) hydrogen bonds : bond 0.06473 / 4.77 ( 496) hydrogen bonds : angle 4.67488 / 3.45 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.258 Fit side-chains REVERT: D 397 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7532 (ttt-90) outliers start: 18 outliers final: 11 residues processed: 73 average time/residue: 0.0788 time to fit residues: 8.8620 Evaluate side-chains 72 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 50.0000 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 50.0000 chunk 67 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.0370 chunk 44 optimal weight: 0.1980 overall best weight: 1.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 383 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.121662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.093426 restraints weight = 33680.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.095403 restraints weight = 18473.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.096723 restraints weight = 12296.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.097619 restraints weight = 9263.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.098282 restraints weight = 7593.246| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10135 Z= 0.188 Angle : 0.670 9.564 14797 Z= 0.407 Chirality : 0.042 0.196 1755 Planarity : 0.004 0.073 1186 Dihedral : 30.044 144.199 3328 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 7.01 % Allowed : 27.10 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.30), residues: 829 helix: -0.18 (0.25), residues: 437 sheet: -1.09 (0.40), residues: 122 loop : -1.04 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.022 0.002 TYR B 373 PHE 0.037 0.002 PHE A 367 TRP 0.011 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.19 (10135) covalent geometry : angle 0.66975 / 0.41 (14797) hydrogen bonds : bond 0.06093 / 4.50 ( 496) hydrogen bonds : angle 4.44652 / 3.28 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.346 Fit side-chains REVERT: D 397 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7300 (ttt-90) outliers start: 15 outliers final: 14 residues processed: 71 average time/residue: 0.0719 time to fit residues: 8.2020 Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.121879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.098162 restraints weight = 34381.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.099018 restraints weight = 25520.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099162 restraints weight = 20775.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.099388 restraints weight = 14638.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.099535 restraints weight = 13418.520| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10135 Z= 0.178 Angle : 0.659 9.364 14797 Z= 0.399 Chirality : 0.041 0.200 1755 Planarity : 0.004 0.070 1186 Dihedral : 30.042 144.885 3328 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.44 % Favored : 91.44 % Rotamer: Outliers : 8.41 % Allowed : 26.64 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.30), residues: 829 helix: -0.04 (0.26), residues: 439 sheet: -1.13 (0.40), residues: 122 loop : -0.95 (0.43), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 337 TYR 0.018 0.002 TYR B 364 PHE 0.031 0.002 PHE A 367 TRP 0.014 0.001 TRP B 348 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.18 (10135) covalent geometry : angle 0.65854 / 0.40 (14797) hydrogen bonds : bond 0.05726 / 4.26 ( 496) hydrogen bonds : angle 4.23507 / 3.12 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.270 Fit side-chains REVERT: D 397 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7126 (ttt-90) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.0770 time to fit residues: 8.9597 Evaluate side-chains 77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 363 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0570 chunk 33 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 chunk 67 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 overall best weight: 4.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.118129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.093622 restraints weight = 35100.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.093014 restraints weight = 32470.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.093949 restraints weight = 26675.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.093972 restraints weight = 18587.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.094740 restraints weight = 17452.411| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.129 10135 Z= 0.409 Angle : 0.893 13.862 14797 Z= 0.513 Chirality : 0.052 0.295 1755 Planarity : 0.006 0.069 1186 Dihedral : 30.260 144.319 3328 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 10.28 % Allowed : 24.30 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.28), residues: 829 helix: -0.83 (0.24), residues: 440 sheet: -1.60 (0.40), residues: 122 loop : -1.56 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 375 TYR 0.017 0.003 TYR B 364 PHE 0.021 0.003 PHE D 395 TRP 0.020 0.002 TRP B 366 HIS 0.014 0.002 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.41 (10135) covalent geometry : angle 0.89295 / 0.51 (14797) hydrogen bonds : bond 0.09897 / 7.33 ( 496) hydrogen bonds : angle 5.27591 / 3.85 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.266 Fit side-chains REVERT: A 335 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8328 (t0) REVERT: D 397 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7692 (ttt-90) outliers start: 22 outliers final: 20 residues processed: 72 average time/residue: 0.0723 time to fit residues: 8.2395 Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 377 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 20.0000 chunk 1 optimal weight: 0.0040 chunk 0 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 0.0020 chunk 45 optimal weight: 20.0000 chunk 16 optimal weight: 50.0000 chunk 47 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.121968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.098513 restraints weight = 33832.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.098978 restraints weight = 22472.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.099578 restraints weight = 18152.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.099593 restraints weight = 13626.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.099877 restraints weight = 12420.910| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10135 Z= 0.163 Angle : 0.676 10.233 14797 Z= 0.408 Chirality : 0.042 0.198 1755 Planarity : 0.005 0.067 1186 Dihedral : 30.153 145.423 3328 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 5.61 % Allowed : 28.97 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.30), residues: 829 helix: -0.16 (0.25), residues: 439 sheet: -1.46 (0.40), residues: 122 loop : -0.93 (0.44), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 337 TYR 0.027 0.002 TYR B 373 PHE 0.024 0.002 PHE C 340 TRP 0.019 0.001 TRP B 348 HIS 0.008 0.001 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (10135) covalent geometry : angle 0.67562 / 0.41 (14797) hydrogen bonds : bond 0.05986 / 4.51 ( 496) hydrogen bonds : angle 4.35901 / 3.22 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.260 Fit side-chains REVERT: D 397 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7207 (ttt-90) REVERT: B 352 GLU cc_start: 0.4266 (OUTLIER) cc_final: 0.3865 (pt0) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 0.0587 time to fit residues: 6.8830 Evaluate side-chains 75 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0470 chunk 12 optimal weight: 40.0000 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 21 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.119340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.095201 restraints weight = 34018.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.095936 restraints weight = 24028.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.096198 restraints weight = 19010.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.096359 restraints weight = 14379.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.096434 restraints weight = 13404.506| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 10135 Z= 0.288 Angle : 0.754 11.453 14797 Z= 0.443 Chirality : 0.045 0.225 1755 Planarity : 0.005 0.069 1186 Dihedral : 30.221 144.995 3328 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 7.01 % Allowed : 28.04 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.30), residues: 829 helix: -0.39 (0.25), residues: 436 sheet: -1.54 (0.41), residues: 122 loop : -1.16 (0.42), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 337 TYR 0.035 0.003 TYR B 373 PHE 0.022 0.002 PHE A 367 TRP 0.016 0.002 TRP B 366 HIS 0.011 0.002 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.29 (10135) covalent geometry : angle 0.75416 / 0.44 (14797) hydrogen bonds : bond 0.07561 / 5.59 ( 496) hydrogen bonds : angle 4.66459 / 3.43 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.178 Fit side-chains REVERT: A 335 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8293 (t0) REVERT: D 397 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7695 (ttt-90) outliers start: 15 outliers final: 13 residues processed: 69 average time/residue: 0.0626 time to fit residues: 6.8850 Evaluate side-chains 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASN Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.1980 chunk 52 optimal weight: 0.0770 chunk 64 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 33 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 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 = 0.4164 r_free = 0.4164 target = 0.119491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.095605 restraints weight = 34159.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.096247 restraints weight = 25788.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.096581 restraints weight = 20284.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.096599 restraints weight = 15503.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096753 restraints weight = 14427.688| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 10135 Z= 0.326 Angle : 1.024 59.200 14797 Z= 0.614 Chirality : 0.046 0.277 1755 Planarity : 0.005 0.067 1186 Dihedral : 30.225 145.015 3328 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 7.01 % Allowed : 27.57 % Favored : 65.42 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.30), residues: 829 helix: -0.39 (0.25), residues: 436 sheet: -1.55 (0.41), residues: 122 loop : -1.18 (0.42), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 337 TYR 0.028 0.003 TYR B 373 PHE 0.020 0.002 PHE A 367 TRP 0.016 0.001 TRP B 366 HIS 0.010 0.002 HIS B 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.33 (10135) covalent geometry : angle 1.02442 / 0.61 (14797) hydrogen bonds : bond 0.07550 / 5.59 ( 496) hydrogen bonds : angle 4.66570 / 3.43 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1511.45 seconds wall clock time: 26 minutes 49.77 seconds (1609.77 seconds total)