Starting phenix.real_space_refine on Thu Mar 13 23:52:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srp_40737/03_2025/8srp_40737.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srp_40737/03_2025/8srp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8srp_40737/03_2025/8srp_40737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srp_40737/03_2025/8srp_40737.map" model { file = "/net/cci-nas-00/data/ceres_data/8srp_40737/03_2025/8srp_40737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srp_40737/03_2025/8srp_40737.cif" } resolution = 3.7 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 6, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 6.85, per 1000 atoms: 0.72 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: 2.25 Conformation dependent library (CDL) restraints added in 749.3 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: 3.66 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: 2.77 Time building geometry restraints manager: 2.69 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=" CG PRO C 354 " pdb=" CD PRO C 354 " ideal model delta sigma weight residual 1.503 1.418 0.085 3.40e-02 8.65e+02 6.26e+00 bond pdb=" CB PRO C 354 " pdb=" CG PRO C 354 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.23e+00 bond pdb=" N PRO C 354 " pdb=" CD PRO C 354 " ideal model delta sigma weight residual 1.473 1.492 -0.019 1.40e-02 5.10e+03 1.77e+00 bond pdb=" C ALA B 353 " pdb=" N PRO B 354 " ideal model delta sigma weight residual 1.340 1.374 -0.034 2.76e-02 1.31e+03 1.53e+00 bond pdb=" C3' DT M 16 " pdb=" C2' DT M 16 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 10130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 14760 3.23 - 6.47: 32 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=" N PRO C 354 " pdb=" CD PRO C 354 " pdb=" CG PRO C 354 " ideal model delta sigma weight residual 103.20 96.85 6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" CA LEU C 360 " pdb=" CB LEU C 360 " pdb=" CG LEU C 360 " ideal model delta sigma weight residual 116.30 127.68 -11.38 3.50e+00 8.16e-02 1.06e+01 angle pdb=" C ALA C 353 " pdb=" N PRO C 354 " pdb=" CD PRO C 354 " ideal model delta sigma weight residual 125.00 111.72 13.28 4.10e+00 5.95e-02 1.05e+01 angle pdb=" C GLU C 352 " pdb=" N ALA C 353 " pdb=" CA ALA C 353 " ideal model delta sigma weight residual 121.80 129.33 -7.53 2.44e+00 1.68e-01 9.53e+00 ... (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 - 0.026: 1047 0.026 - 0.052: 499 0.052 - 0.078: 138 0.078 - 0.104: 62 0.104 - 0.129: 9 Chirality restraints: 1755 Sorted by residual: chirality pdb=" C1' DC N 20 " pdb=" O4' DC N 20 " pdb=" C2' DC N 20 " pdb=" N1 DC N 20 " both_signs ideal model delta sigma weight residual False 2.47 2.34 0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA VAL A 405 " pdb=" N VAL A 405 " pdb=" C VAL A 405 " pdb=" CB VAL A 405 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA VAL D 405 " pdb=" N VAL D 405 " pdb=" C VAL D 405 " pdb=" CB VAL D 405 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.00e-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: 3.900 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.360 Find NCS groups from input model: 0.510 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.004 0.114 10135 Z= 0.229 Angle : 0.658 16.173 14797 Z= 0.395 Chirality : 0.035 0.129 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 (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: -1.47 (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 TRP 0.012 0.001 TRP C 348 HIS 0.006 0.001 HIS A 387 PHE 0.014 0.001 PHE A 340 TYR 0.031 0.002 TYR B 330 ARG 0.007 0.001 ARG C 358 *********************** 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 : 0.838 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.1700 time to fit residues: 19.0712 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 : 0.847 ------------------------------------------------------------------------------- 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 84 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.118953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.095136 restraints weight = 35672.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.094858 restraints weight = 33651.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.095482 restraints weight = 27609.073| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.096 10135 Z= 0.594 Angle : 0.829 13.248 14797 Z= 0.486 Chirality : 0.048 0.199 1755 Planarity : 0.007 0.142 1186 Dihedral : 29.751 136.764 3330 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 7.48 % Allowed : 24.30 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.90 (0.28), residues: 829 helix: -1.08 (0.23), residues: 430 sheet: -0.68 (0.43), residues: 122 loop : -1.53 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 366 HIS 0.013 0.002 HIS B 387 PHE 0.019 0.003 PHE B 367 TYR 0.024 0.004 TYR D 364 ARG 0.007 0.001 ARG D 375 *********************** 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 78 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7692 (ttt-90) outliers start: 16 outliers final: 14 residues processed: 73 average time/residue: 0.1635 time to fit residues: 18.3458 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 : 0.722 ------------------------------------------------------------------------------- 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 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 363 ILE Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 398 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 43 optimal weight: 50.0000 chunk 42 optimal weight: 50.0000 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4191 r_free = 0.4191 target = 0.121142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097468 restraints weight = 34719.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.097912 restraints weight = 26710.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.098777 restraints weight = 20299.526| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10135 Z= 0.307 Angle : 0.664 9.343 14797 Z= 0.395 Chirality : 0.038 0.143 1755 Planarity : 0.005 0.110 1186 Dihedral : 29.645 139.648 3328 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.54 % Allowed : 28.97 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 (0.29), residues: 829 helix: -0.37 (0.25), residues: 426 sheet: -0.71 (0.42), residues: 122 loop : -1.27 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 348 HIS 0.007 0.001 HIS B 387 PHE 0.016 0.001 PHE B 340 TYR 0.018 0.002 TYR B 364 ARG 0.007 0.001 ARG A 337 *********************** 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 79 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.649 Fit side-chains REVERT: D 397 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7724 (ttt-90) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.1694 time to fit residues: 18.5581 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 : 0.661 ------------------------------------------------------------------------------- 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 340 PHE 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 396 VAL Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 352 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 20.0000 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 30.0000 chunk 51 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4186 r_free = 0.4186 target = 0.120719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.096566 restraints weight = 33851.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.097186 restraints weight = 24783.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.097894 restraints weight = 19080.891| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10135 Z= 0.341 Angle : 0.671 10.229 14797 Z= 0.399 Chirality : 0.039 0.142 1755 Planarity : 0.005 0.082 1186 Dihedral : 29.590 140.046 3328 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 8.88 % Allowed : 27.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.29), residues: 829 helix: -0.30 (0.25), residues: 433 sheet: -0.83 (0.41), residues: 122 loop : -1.24 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 366 HIS 0.008 0.001 HIS B 387 PHE 0.015 0.001 PHE B 340 TYR 0.019 0.002 TYR B 364 ARG 0.004 0.000 ARG B 397 *********************** 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 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.739 Fit side-chains REVERT: D 397 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7757 (ttt-90) outliers start: 19 outliers final: 14 residues processed: 73 average time/residue: 0.1665 time to fit residues: 19.3758 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 : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 0.0470 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4200 r_free = 0.4200 target = 0.121570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.097670 restraints weight = 33700.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.097875 restraints weight = 22907.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.099035 restraints weight = 17912.051| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10135 Z= 0.278 Angle : 0.643 9.459 14797 Z= 0.383 Chirality : 0.037 0.132 1755 Planarity : 0.004 0.079 1186 Dihedral : 29.544 141.066 3328 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 7.94 % Allowed : 27.57 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.30), residues: 829 helix: -0.10 (0.26), residues: 437 sheet: -0.93 (0.41), residues: 122 loop : -1.07 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 PHE 0.021 0.001 PHE A 367 TYR 0.018 0.002 TYR B 364 ARG 0.006 0.001 ARG A 386 *********************** 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 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.723 Fit side-chains REVERT: D 397 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7474 (ttt-90) outliers start: 17 outliers final: 14 residues processed: 74 average time/residue: 0.1718 time to fit residues: 19.6113 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 : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 THR 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 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 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 26 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 47 optimal weight: 30.0000 chunk 92 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 50.0000 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4193 r_free = 0.4193 target = 0.121165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.097286 restraints weight = 33776.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.097467 restraints weight = 24306.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.098565 restraints weight = 19403.682| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10135 Z= 0.302 Angle : 0.654 10.249 14797 Z= 0.389 Chirality : 0.038 0.136 1755 Planarity : 0.004 0.071 1186 Dihedral : 29.527 141.889 3328 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 8.88 % Allowed : 25.23 % 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 (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: -0.93 (0.30), residues: 829 helix: -0.07 (0.26), residues: 439 sheet: -1.05 (0.41), residues: 122 loop : -1.05 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 366 HIS 0.007 0.001 HIS B 387 PHE 0.023 0.002 PHE A 367 TYR 0.017 0.002 TYR B 364 ARG 0.006 0.000 ARG A 337 *********************** 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 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.848 Fit side-chains REVERT: D 397 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7557 (ttt-90) outliers start: 19 outliers final: 17 residues processed: 73 average time/residue: 0.2066 time to fit residues: 23.2908 Evaluate side-chains 80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 39 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.0030 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.123083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.100690 restraints weight = 34978.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.100941 restraints weight = 25140.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.102870 restraints weight = 18545.683| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10135 Z= 0.189 Angle : 0.608 8.337 14797 Z= 0.362 Chirality : 0.035 0.135 1755 Planarity : 0.004 0.067 1186 Dihedral : 29.459 143.253 3328 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.61 % Allowed : 28.50 % 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 (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: -0.57 (0.31), residues: 829 helix: 0.27 (0.26), residues: 439 sheet: -1.03 (0.41), residues: 122 loop : -0.91 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 348 HIS 0.005 0.001 HIS A 387 PHE 0.012 0.001 PHE A 367 TYR 0.016 0.001 TYR B 364 ARG 0.005 0.001 ARG A 337 *********************** 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 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: D 397 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7309 (ttt-90) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.2922 time to fit residues: 33.0982 Evaluate side-chains 76 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 340 PHE 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 352 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.122046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.098722 restraints weight = 35371.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099013 restraints weight = 26361.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.099856 restraints weight = 21600.163| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10135 Z= 0.242 Angle : 0.619 10.151 14797 Z= 0.368 Chirality : 0.036 0.135 1755 Planarity : 0.004 0.064 1186 Dihedral : 29.419 143.687 3328 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 6.54 % Allowed : 28.50 % 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 (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: -0.55 (0.31), residues: 829 helix: 0.30 (0.26), residues: 439 sheet: -1.09 (0.42), residues: 122 loop : -0.90 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 366 HIS 0.005 0.001 HIS B 387 PHE 0.017 0.001 PHE A 367 TYR 0.019 0.002 TYR B 373 ARG 0.006 0.000 ARG A 337 *********************** 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: 14 poor density : 65 time to evaluate : 0.676 Fit side-chains REVERT: A 397 ARG cc_start: 0.7593 (ttm170) cc_final: 0.7226 (ttt180) REVERT: D 397 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7287 (ttt-90) outliers start: 14 outliers final: 13 residues processed: 71 average time/residue: 0.1664 time to fit residues: 18.1318 Evaluate side-chains 78 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 397 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 340 PHE 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 352 GLU Chi-restraints excluded: chain B residue 398 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.118202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094213 restraints weight = 35535.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094471 restraints weight = 27654.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.095301 restraints weight = 19856.951| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 10135 Z= 0.508 Angle : 0.767 12.761 14797 Z= 0.451 Chirality : 0.045 0.216 1755 Planarity : 0.006 0.065 1186 Dihedral : 29.591 143.545 3328 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 7.94 % Allowed : 28.04 % Favored : 64.02 % 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: -1.30 (0.30), residues: 829 helix: -0.32 (0.25), residues: 435 sheet: -1.37 (0.41), residues: 122 loop : -1.24 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 366 HIS 0.011 0.002 HIS B 387 PHE 0.018 0.002 PHE C 395 TYR 0.036 0.004 TYR B 373 ARG 0.009 0.001 ARG D 386 *********************** 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: 17 poor density : 60 time to evaluate : 0.721 Fit side-chains REVERT: D 397 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7767 (ttt-90) outliers start: 17 outliers final: 16 residues processed: 69 average time/residue: 0.1556 time to fit residues: 17.0767 Evaluate side-chains 75 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 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 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.0010 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.121166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.098039 restraints weight = 35486.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.098532 restraints weight = 26544.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.098733 restraints weight = 22342.363| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10135 Z= 0.233 Angle : 0.635 8.669 14797 Z= 0.378 Chirality : 0.037 0.131 1755 Planarity : 0.004 0.065 1186 Dihedral : 29.506 144.342 3328 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.14 % Allowed : 30.84 % Favored : 64.02 % 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: -0.80 (0.31), residues: 829 helix: 0.06 (0.26), residues: 433 sheet: -1.30 (0.41), residues: 122 loop : -0.86 (0.43), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 348 HIS 0.006 0.001 HIS B 387 PHE 0.017 0.001 PHE A 367 TYR 0.034 0.002 TYR B 373 ARG 0.006 0.001 ARG A 337 ********************** 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 74 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.840 Fit side-chains REVERT: D 397 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7277 (ttt-90) outliers start: 11 outliers final: 10 residues processed: 69 average time/residue: 0.2011 time to fit residues: 22.6141 Evaluate side-chains 73 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 394 CYS 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 335 ASN Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 398 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 87 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 46 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 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 = 0.4229 r_free = 0.4229 target = 0.123559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.100252 restraints weight = 34149.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.100561 restraints weight = 23652.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.102251 restraints weight = 16914.989| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10135 Z= 0.188 Angle : 0.600 7.156 14797 Z= 0.358 Chirality : 0.034 0.131 1755 Planarity : 0.004 0.061 1186 Dihedral : 29.360 145.911 3328 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.67 % Allowed : 31.31 % Favored : 64.02 % 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: -0.44 (0.31), residues: 829 helix: 0.40 (0.27), residues: 433 sheet: -1.16 (0.42), residues: 122 loop : -0.77 (0.43), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 348 HIS 0.007 0.001 HIS A 387 PHE 0.013 0.001 PHE C 340 TYR 0.028 0.002 TYR B 373 ARG 0.007 0.001 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.02 seconds wall clock time: 48 minutes 57.75 seconds (2937.75 seconds total)